UNITED STATES SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-Q

(Mark One)


þ		Quarterly Report Pursuant to Section 13 or 15 (d) of the Securities Exchange Act of 1934

For the quarterly period ended ~~June~~March 3031, ~~2006~~2009.


o		Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the transition period from to .

Commission file number 001-32629

AVALON PHARMACEUTICALS, INC.

(Exact Name of Registrant as Specified in Its Charter)


Delaware		52-2209310
(State or Other Jurisdiction of		(I.R.S. Employer Identification No.)
Incorporation or Organization)

20358 Seneca Meadows Parkway
Germantown, Maryland		20876
(Address of Principal Executive Offices)		(Zip Code)

Registrant’s Telephone Number, Including Area Code: (301) 556-9900

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No o

Indicate by check mark whether the registrant ishas asubmitted ~~large~~electronically ~~accelerated~~and ~~filer~~posted on its corporate Web site, orif aany, ~~non-accelerated filer.~~every ~~See~~Interactive ~~definition~~Data ofFile ~~“accelerated~~required ~~filer~~to ~~and~~be ~~large~~submitted ~~accelerated~~and ~~filer”~~posted pursuant into Rule ~~12b-2~~405 of Regulation S-T during the ~~Exchange~~ ~~Act.~~preceding 12 months (~~Check~~or ~~one~~for such shorter period that the registrant was required to submit and post such files):. Yes o No o

~~Large~~ Indicate by check mark whether the registrant is a large accelerated filer, oan ~~Accelerated~~ accelerated filer, oa ~~Non~~non-accelerated filer, þor a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):


Large accelerated filer o	Accelerated filer o	Non-accelerated filer o	Smaller reporting company þ
		(Do not check if a smaller reporting company)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No þ

As of ~~August~~May 118, ~~2006~~2009, 1020,~~110~~428,~~028~~475 shares of Avalon Pharmaceuticals, Inc. common stock, par value $.01 per share, were outstanding.

AVALON PHARMACEUTICALS, INC.

	Page
PART I. FINANCIAL INFORMATION		2
Item 1. Financial Statements		21
Balance Sheets as of June 30, 2006 (unaudited) and December 31, 2005		2
Balance Sheets as of March 31, 2009 (unaudited) and December 31, 2008		1
Statements of Operations for the three and six months ended June 30, 2006 and 2005 (unaudited)		3
Statements of Operations for the three months ended March 31, 2009 and 2008 (unaudited)		2
Statements of Cash Flows for the six months ended June 30, 2006 and 2005 (unaudited)		4
Statements of Cash Flows for the three months ended March 31, 2009 and 2008 (unaudited)		3
Notes to Financial Statements (unaudited)		54
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		910
Item 3. Quantitative and Qualitative Disclosures About Market Risk		13
Item 4. Controls and Procedures		13
Item 4T. Controls and Procedures		13
PART II. OTHER INFORMATION		14
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds		14
Item 6. Exhibits		14
Item 4. Submission of Matters to a Vote of Security Holders		14
SIGNATURES		15
Item 6. Exhibits		15
SIGNATURES		16

FORWARD-LOOKING STATEMENTS

From time to time in this interim quarterly report we may make statements that reflect our current expectations regarding our future results of operations, economic performance, and financial condition, as well as other matters that may affect our business. In general, we try to identify these forward-looking statements by using words such as “anticipate,” “believe,” “expect,” “estimate,” and similar expressions.

All of these items involve significant risks and uncertainties. These and any of the other statements we make in this quarterly report that are forward-looking are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. We caution you that our actual results may differ significantly from the results we discuss in the forward-looking statements.

We discuss some factors that could cause or contribute to such differences in the “Risk Factors” section of our Annual Report on Form 10-K for the fiscal year ended December 31, ~~2005~~2008. In addition, any forward-looking statements we make in this document speak only as of the date of this document, and we do not intend to update any such forward-looking statements to reflect events or circumstances that occur after that date.

~~Page 1~~ii

PART I. FINANCIAL INFORMATION

Item 1. Financial Statements ~~(unaudited)~~

AVALON PHARMACEUTICALS, INC. ~~BALANCE SHEETS (in thousands)~~

	June 30,			December 31,
	2006			2005
	(Unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	4,366		$	9,733
Short-term marketable securities		16,136			10,922
Accounts receivable		218			794
Interest receivable		281			201
Prepaid expenses		777			833
Deposits		—			102
Total current assets		21,778			22,584
Restricted cash and marketable securities		5,520			6,313
Property and equipment, net		9,843			10,997
Long-term marketable securities		781			781
Deposits		205			205
Deferred financing costs		453			402
Total assets	$	38,580		$	41,282
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	586		$	1,098
Accrued expenses and other current liabilities		748			913
Deferred revenue		1,923			1,273
Current portion on long-term debt		1,886			2,230
Total current liabilities		5,143			5,514
Deferred rent		469			468
Long-term deferred revenue, net of current portion		300			650
Long-term debt, net of current portion		7,267			8,714
Other long-term liabilities		—			53
Stockholders’ equity:
Common stock, $0.01 par value; 60,000,000 shares authorized; 10,102,836 and 8,407,376 shares issued and outstanding at June 30, 2006 and December 31, 2005, respectively.		101			84
Additional capital		119,941			111,677
Deferred stock compensation		—			(250	)
Other comprehensive loss		(51	)		(26	)
Accumulated deficit		(94,590	)		(85,602	)
Total stockholders’ equity		25,401			25,883
Total liabilities and stockholders’ equity	$	38,580		$	41,282

BALANCE SHEETS

(in thousands, except share amounts)


	March 31,			December 31,
	2009			2008
	(Unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	3,458		$	4,890
Short-term marketable securities		—			900
Accounts receivable		25			13
Interest receivable		—			11
Prepaid expenses		439			358
Deposits & Other Current Assets		—			22


Total current assets		3,922			6,194
Property and equipment, net		5,574			5,950


Total assets	$	9,496		$	12,144


LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Short-term note payable	$	4,000		$	3,000
Accounts payable		1,684			1,627
Accrued expenses and other current liabilities		246			385
Deferred revenue and customer advances		1,884			1,884


Total current liabilities		7,814			6,896
Deferred rent		393			404
Stockholders’ equity:
Series C Junior Participating Preferred stock, $0.01 par value, 300,000 shares authorized, no shares issued and outstanding		—			—
Common stock, $0.01 par value; 60,000,000 shares authorized; 20,428,475 shares issued and outstanding at March 31, 2009 and December 31, 2008		204			204
Additional capital		150,892			150,844
Accumulated deficit		(149,807	)		(146,204	)


Total stockholders’ equity		1,289			4,844


Total liabilities and stockholders’ equity	$	9,496		$	12,144

See accompanying notes.

~~Page 2~~1

AVALON PHARMACEUTICALS, INC. ~~STATEMENTS OF OPERATIONS (in thousands, except share and per share amounts) (Unaudited)~~

	Three Months Ended						Six Months Ended
	June 30,						June 30,
	2006			2005			2006			2005
Revenues	$	417		$	—		$	956		$	—
Costs and expenses:
Research and development		3,338			2,621			6,487			10,013
General and administrative		1,795			1,285			4,048			2,450
Total costs and expenses		5,133			3,906			10,535			12,463
Loss from operations		(4,716	)		(3,906	)		(9,579	)		(12,463	)
Other income (expense):
Interest income		335			83			670			163
Interest expense		(204	)		(313	)		(424	)		(602	)
Other		156			157			346			222
Total other income (expense):		287			(72	)		592			(218	)
Net loss	$	(4,429	)	$	(3,979	)	$	(8,987	)	$	(12,680	)
Accretion of redeemable convertible preferred stock issuance costs		—			(370	)		—			(741	)
Net loss attributed to common stockholders	$	(4,429	)	$	(4,349	)	$	(8,987	)	$	(13,421	)
Net loss attributed to common stockholders per common share — basic and diluted	$	(0.44	)	$	(33.56	)	$	(0.94	)	$	(103.92	)
Weighted average number of common share — basic and diluted		10,100,052			129,597			9,557,757			129,147

STATEMENTS OF OPERATIONS

(in thousands, except share and per share amounts)
(Unaudited)


	Three Months Ended
	March 31,
	2009			2008
Revenues	$	—		$	50

Costs and expenses:
Research and development		2,709			4,360
General and administrative		921			2,133


Total costs and expenses		3,630			6,493


Loss from operations		(3,630	)		(6,443	)

Other income (expense):
Interest income		—			307
Interest expense		(52	)		(115	)
Other		80			2


Total other income (expense):		28			194


Net loss	$	(3,602	)	$	(6,249	)


Net loss per share — basic and diluted	$	(0.18	)	$	(0.37	)


Weighted average number of shares — basic and diluted		20,428,475			17,029,837

See accompanying notes.

~~Page 3~~2

AVALON PHARMACEUTICALS, INC. ~~STATEMENTS OF CASH FLOWS (in thousands) (Unaudited)~~

	Six Months Ended
	June 30,
	2006			2005
Operating activities
Net loss	$	(8,987	)	$	(12,680	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation		1,209			1,351
Non-cash interest expense		153			(58	)
Amortization of premium on investments		38			47
Compensation expense related to stock and stock options		1,291			80
Changes in operating assets and liabilities:
Prepaid expenses		56			(26	)
Accounts receivable and other assets		598			(51	)
Accounts payable		(513	)		2,483
Accrued liabilities		(217	)		67
Deferred revenue		299			1,892
Deferred rent		1			12
Net cash used in operating activities		(6,072	)		(6,883	)
Investing activities
Proceeds from the sale of marketable securities		6,673			11,339
Purchases of marketable securities		(11,157	)		(6,229	)
Purchases of property and equipment		(55	)		(6	)
Net cash (used in) provided by investing activities		(4,539	)		5,105
Principal payments on line of credit		(591	)		(752	)
Proceeds from issuance of common stock		7,240			16
Payments on bond payable		(1,200	)		(1,200	)
Deferred financing costs		(205	)		(387	)
Proceeds from issuance of convertible notes		—			5,189
Net cash provided by financing activities		5,244			2,866
Net (decrease) increase in cash and cash equivalents		(5,367	)		1,087
Cash and cash equivalents at beginning of period		9,733			2,251
Cash and cash equivalents at end of period	$	4,366		$	3,339

STATEMENTS OF CASH FLOWS

(in thousands)
(Unaudited)


	Three Months Ended
	March 31,
	2009			2008
Operating activities
Net loss	$	(3,602	)	$	(6,249	)

Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation		382			474
Non-cash interest expense		—			53
Amortization of premium on investments		—			(108	)
Stock based compensation		48			219
Changes in operating assets and liabilities:
Prepaid expenses		(81	)		(273	)
Accounts receivable and other assets		21			416
Accounts payable		57			1,409
Accrued expenses and other current liabilities		(139	)		(715	)
Deferred revenue and customer advances		—			(50	)
Deferred rent		(12	)		(7	)


Net cash used in operating activities		(3,326	)		(4,831	)
Investing activities
Proceeds from the sale and maturities of marketable securities		899			9,227
Purchases of marketable securities		—			(4,843	)
Purchases of property and equipment		(5	)		(145	)


Net cash provided by investing activities		894			4,239
Financing activities
Principal payments on debt		—			(11	)
Proceeds from borrowings on note payable		1,000			—
Deferred financing costs		—			(32	)


Net cash provided by (used in) financing activities		1,000			(43	)


Net decrease in cash and cash equivalents		(1,432	)		(635	)
Cash and cash equivalents at beginning of period		4,890			6,276


Cash and cash equivalents at end of period	$	3,458		$	5,641

See accompanying notes.

~~Page 4~~3

AVALON PHARMACEUTICALS, INC. ~~NOTES TO FINANCIAL STATEMENTS (UNAUDITED)~~

~~The~~NOTES ~~financial~~TO ~~statements~~FINANCIAL included in this report have been prepared, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission. Certain information and footnote disclosures, normally included in financial statements prepared in accordance with U.S. generally accepted accounting principles, have been condensed or omitted pursuant to such rules and regulations. These financial statements should be read in conjunction with the audited financial statements and the related notes included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2005. STATEMENTS

InMARCH ~~the opinion of our management~~31, any adjustments contained in the accompanying unaudited financial statements as of and for the three and six months ended June 30, 2006 and 2005 are of a normal recurring nature, except for the adjustments required to implement FASB Statement No. 123(R), and are necessary to present fairly our financial position, results of operations and cash flows. Interim results are not necessarily indicative of results for the full fiscal year. 2009

~~1. Organization~~ (UNAUDITED)

~~Avalon Pharmaceuticals, Inc~~1. ~~(“Avalon,”~~Basis ~~or the “Company”), was incorporated on November 10, 1999, under the laws~~ of ~~the state of Delaware. The Company is a biopharmaceutical company focused~~Presentation ~~on the discovery and development of small molecule therapeutics for the treatment of cancer.~~

2 The financial statements included in this report have been prepared, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission. ~~Summary~~Certain information and footnote disclosures, normally included in financial statements prepared in accordance with U.S. generally accepted accounting principles, have been condensed or omitted pursuant to such rules and regulations. These financial statements should be read in conjunction with the audited financial statements and the related notes included in the Annual Report on Form 10-K of ~~Significant~~Avalon Pharmaceuticals, ~~Accounting~~Inc. ~~Policies~~(“Avalon” or the “Company”) for the fiscal year ended December 31, 2008.

In the opinion of Avalon’s management, any adjustments contained in the accompanying unaudited financial statements as of and for the three months ended March 31, 2009 and 2008 are of a normal recurring nature and are necessary to present fairly the Company’s financial position, results of operations and cash flows. Interim results are not necessarily indicative of results for the full fiscal year.

2. Liquidity Risks and Management’s Plans

The accompanying financial statements have been prepared on a going-concern basis, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. Since inception, the Company has incurred, and continues to incur, significant losses from operations. As described below in Note 3, the Company entered into an Agreement and Plan of Merger and Reorganization, dated October 27, 2008, as amended (the “Merger Agreement”), with Clinical Data, Inc., a Delaware corporation (“Clinical Data”), and API Acquisition Sub II, LLC, a Delaware limited liability company and an indirect wholly-owned subsidiary of Clinical Data (“API”). The Merger Agreement provides that, upon the terms and subject to the conditions set forth in the Merger Agreement, API will be merged with and into Avalon, with Avalon continuing as the surviving corporation and a wholly-owned subsidiary of Clinical Data (the “Merger”). Management estimates that its existing capital resources will be sufficient to fund the Company’s current operations through the end of the May 2009, prior to which time the Merger with Clinical Data is expected to close.

If the Merger does not close by the end of May 2009, the Company’s ability to continue as a going concern would be dependent on management’s ability to raise additional capital sufficient to meet the Company’s obligations on a timely basis, and to ultimately attain profitability. In light of the proposed Merger, the Company’s management does not expect to seek to raise additional capital. Should the Merger not close or if the closing is delayed beyond the end of May 2009, there is no assurance that the Company would be able to raise capital sufficient to enable the Company to continue its operations significantly beyond the end of May 2009.

In the event the Company were unable to successfully raise additional capital in such circumstances, the Company will not have sufficient cash flows and liquidity to finance its business operations as currently contemplated. Accordingly, in such circumstances the Company would be compelled to reduce general and administrative expenses and delay research and development projects and the purchase of scientific equipment and supplies until it were able to obtain sufficient financing.

Failure to close the Merger, a delay in the expected timing of the closing of the Merger, or failure to raise additional capital would significantly limit the Company’s ability to continue as a going concern. The balance sheets do not include any adjustments relating to recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might be necessary should the Company be unable to continue in existence.

3. Clinical Data Merger

On October 27, 2008, the Company entered into the Merger Agreement with Clinical Data and API. The Merger Agreement was subsequently amended on January 12, 2009 and March 30, 2009. The Merger Agreement provides that API will be merged with and into the Company, with the Company continuing as the surviving corporation and an indirect wholly-owned subsidiary of Clinical Data. As a condition to Clinical Data and Avalon entering into the Merger Agreement and as part of the proposed merger, on October 27, 2008, the parties entered into a number of other arrangements including a private placement of securities, a license agreement and a secured loan arrangement.

Merger Agreement

Pursuant to the terms of the Merger Agreement, Clinical Data will acquire all of the outstanding shares of Avalon’s common stock for consideration consisting of Clinical Data common stock and certain contingent rights to acquire additional shares of Clinical Data common stock. Shares of Avalon common stock held by Clinical Data and its subsidiaries, will be cancelled without consideration at the closing (the “Closing”). Upon the closing of the Merger, each outstanding share of Avalon common stock shall be converted into a right to receive 0.0470 shares of Clinical Data common stock and a contingent value right (a “CVR”) to receive an additional fraction of a share of Clinical Data common stock upon the achievement of defined milestones.

If the Merger Agreement is terminated under specified circumstances, Avalon may be required to pay Clinical Data a termination fee of $300,000 and reimburse Clinical Data up to $100,000 for its expenses associated with the Merger Agreement.

Rights Plan Amendment

On October 27, 2008, the Company amended its Rights Agreement dated April 26, 2007 to render it inapplicable to the Merger, the transactions contemplated by the Merger Agreement, and the private placement described below.

Private Placement

In connection with the execution of the Merger Agreement and as a part of the proposed merger, Avalon entered into a Securities Purchase Agreement with Clinical Data for the sale of Company common stock and common stock purchase warrants in a private placement for a total purchase price of $237,338. Pursuant to the Securities Purchase Agreement, Clinical Data purchased a total of 3,390,547 shares of the Company’s common stock at a purchase price of $0.07 per share. In addition, the Company issued a common stock purchase warrant exercisable into 1,695,273 shares of common stock. The exercise price of the warrant is $0.86 per share, subject to adjustment for dilutive events. The warrant is not exercisable for six months after issuance and may not be exercised to the extent that the aggregate number of shares of Avalon’s common stock held by Clinical Data following exercise of the warrant (including shares of Avalon common stock otherwise held by Clinical Data) would exceed 19.9% of the outstanding stock of the Company unless the issuance of any additional shares is first approved by a vote of Avalon’s stockholders in accordance with the rules of the NASDAQ Stock Market.

Avalon also entered into a Registration Rights Agreement with Clinical Data contemporaneously with entering into the Securities Purchase Agreement. Pursuant to the Registration Rights Agreement, Avalon agreed to register for resale the shares of common stock issued in the private placement and the shares of common stock issuable upon exercise of the warrant. The Registration Rights Agreement requires Avalon to file the registration statement by November 26, 2008 or Clinical Data shall be entitled to a liquidated damages payment in the amount of 1.5% of the total purchase price of the shares issued in the private placement for each month the registration statement remains unfiled after the deadline. In the event the registration statement is not declared effective by the SEC by the earlier of (i) 90 days after the termination of the Merger Agreement (or 120 days after termination in the event the registration statement is subject to review by the SEC) or (ii) within 5 days following notice from the SEC that the registration statement is no longer subject to review (the “Effectiveness Deadline”), Clinical Data shall be entitled to a liquidated damages payment in the amount of 1.5% of the total purchase price for each month (pro rated for any lesser period) after the Effectiveness Deadline during which such registration statement has not been declared effective by the SEC.

License Agreement

In connection with the execution of the Merger Agreement and as a part of the proposed Merger, the Company entered into a license agreement (the “License Agreement”) with Clinical Data pursuant to which Avalon granted Clinical Data a royalty-free, fully-paid, worldwide, perpetual, irrevocable, sublicensable and exclusive license to AvalonRx ®, Avalon’s proprietary drug-development platform, in exchange for a one time payment of $1,000,000. The license is subject to certain exceptions pursuant to which Avalon retained the right to utilize AvalonRx ® to fulfill its obligations under its existing collaboration agreements and to continue development of AVN 944 and certain of its existing development programs.

Secured Loan

As part of the proposed Merger, Avalon entered into a Note Purchase Agreement (the “Note Purchase Agreement”) with Clinical Data pursuant to which Clinical Data made a series of loans to Avalon evidenced by term notes (the “Term Notes”) in the aggregate principal amount of $4 million (the “Secured Loan”). The Term Notes bear interest at a fixed rate of 7% per annum and mature on May 31, 2009 unless accelerated pursuant to their terms. The original amount of the Secured Loan under the Note Purchase Agreement was $3 million and matured on March 31, 2009. On January 12, 2009, Clinical Data extended the maturity of the original $3 million Term Note evidencing the Secured Loan until April 30, 2009. On March 30, 2009, Avalon and Clinical Data amended the Note Purchase Agreement and the original $3 million Term Note to further extend the $3 million Term Note’s maturity date to May 31, 2009 and Clinical Data and Avalon also increased the amount borrowed by Avalon under the Note Purchase Agreement from $3 million to $4 million through the issuance by Avalon of an additional $1 million Term Note. The Company has the right to prepay the Term Notes, together with any accrued interest, at any time without penalty. The maturity of the Term Notes accelerates if there is a default under the terms of the Note Purchase Agreement or related documents, including any default, breach or termination of the License Agreement or of the Merger Agreement (other than a termination of the Merger Agreement as a result of a failure to obtain the approval by Avalon’s stockholders of the Merger). The Term Notes are secured by collateral consisting of certain intellectual property rights of Avalon.

4. Organization

Avalon was incorporated on November 10, 1999, under the laws of the state of Delaware. Avalon is a biopharmaceutical company using proprietary technology, AvalonRx ^® , to discover and develop novel therapeutics.

5. Recent Accounting Pronouncements

In June 2008, the FASB ratified EITF Issue No. 07-5, “Determining Whether an Instrument (or an Embedded Feature) is indexed to an Entity’s Own Stock” (EITF 07-5), which supersedes EITF Issue No. 01-6, “The Meaning of ‘Indexed to a Company’s Own Stock’”. SFAS No. 133 specifies that a contract issued or held by a company that is both indexed to its own stock and classified in stockholders’ equity is not considered a derivative instrument for purposes of applying SFAS No. 133. EITF 07-5 provides guidance for applying the requirements of SFAS No. 133, requiring that both an instrument’s contingent exercise provisions and its settlement provisions be evaluated to determine whether the instrument (or embedded feature) is indexed solely to an entity’s own stock. The EITF is effective for financial statements issued for fiscal years beginning after December 15, 2008, and interim periods within those fiscal years. The adoption of EITF 07-5 on January 1, 2009 did not have a material impact on the Company’s results of operations, cash flows or financial positions.

6. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates.

Cash and Cash Equivalents

The Company considers all highly liquid investments with a maturity of three months or less when purchased to be cash equivalents. Cash equivalents consist primarily of money market funds and commercial paper. The Company maintains cash balances with financial institutions in excess of insured limits. The Company does not anticipate any losses with such cash balances.

Marketable Securities

Marketable securities consist primarily of U.S. Treasury, agency and corporate debt securities with various maturities. Management classifies the Company’s marketable securities as available-for-sale. Such securities are stated at market value, with the unrealized gains and losses included as accumulated other comprehensive income (loss). Realized gains and losses and declines in value judged to be other-than-temporary on securities available for sale, if any, are included in operations. A decline in the market value of any available-for-sale security below cost that is deemed to be other-than-temporary results in a reduction in fair value. The impairment is charged to earnings, and a new cost basis for the security is established. Dividend and interest income are recognized when earned. The cost of securities sold is calculated using the specific identification method.

Revenue Recognition

~~Revenues~~ Revenue ~~are~~is recognized when there is persuasive evidence that an ~~arrangement~~agreement exists, delivery ~~has~~ has occurred, the price is fixed and determinable, and collection is reasonably assured. Payments received in advance of work performed are recorded as deferred revenue and recognized ratably over the performance period. Milestone payments are recognized as revenue ~~in an amount commensurate with the level of effort expended~~ when ~~the~~ milestones ~~are achieved~~, ~~contract partner acknowledges completion of the milestone, no further performance obligations exist~~ as defined in the ~~agreements~~contract, ~~collection~~ isare ~~reasonably assured and substantive effort was necessary to achieve the milestone~~achieved. During the first ~~six~~three months of ~~2006~~2008, the Company recognized revenue from ~~the~~work ~~amortization~~performed ~~of up-front~~on ~~payments,~~its ~~work~~collaboration ~~performed~~agreement with Novartis, and ~~expenses~~recognized ~~incurred~~no onrevenue from its other collaboration agreements.

~~Following a review of our collaboration agreements, we have determined that we prematurely~~6 recorded an aggregate of $535,000 of revenue in prior quarters under our agreement with MedImmune. An adjustment to reduce revenue by $535,000 was made in the second quarter of 2006 to reflect properly total revenue recorded through June 30, 2006 under this agreement.

Research and Development Costs

~~The~~ Expenditures, ~~Company~~other ~~expenses~~than ~~its~~advance payments for research and development, ~~costs~~subject to the provisions of EITF 07-03, are expensed as incurred.

Restricted Cash and Investments

In accordance with the terms of a financing arrangement with the Maryland Industrial Development Financing Authority (MIDFA) and Manufacturers and Traders Trust Company (M&T Bank), in order to finance the build out of the Company’s corporate headquarters and research facility located in Germantown, Maryland, the Company established an investment account which is pledged as collateral for a letter of credit. The issuer of the letter of credit, M&T Bank, maintains the investment account. M&T Bank’s security interest in the account cannot exceed the minimum required cash collateral amount, which as of June 30, 2006, was defined as an adjusted market value of $5.5 million. This collateral agreement defines adjusted market value as the product of the fair market value of each permitted investment by a defined percentage ranging from 60% to 100%, depending on the nature of the permitted investment. The minimum cash collateral amount automatically decreases each April 1 as specified in the collateral agreement.

Page 5

Comprehensive Income

SFAS No. 130, Reporting Comprehensive Income, requires the presentation of comprehensive income or loss and its components as part of the financial statements. For the ~~six~~three months ended ~~June~~March 3031, ~~2006~~2009 and ~~2005~~2008, the Company’s net loss plus its unrealized gains (losses) on available-for-sale securities reflects comprehensive income (loss).

Stock-Based Compensation

~~Prior~~ The ~~to January 1, 2006, the~~ Company ~~accounted~~accounts for ~~its stock~~share-based ~~compensation~~payments ~~plans~~in ~~under the~~accordance ~~recognition~~with and measurement provisions of Accounting Principles Board Opinion No. 25, “Accounting for Stock Issued to Employees” (“Opinion 25”), and related Interpretations, as permitted by FASB Statement No. 123,” “Accounting for Stock-Based Compensation” (“Statement 123”). Effective January 1, 2006, the ~~Company adopted the fair value recognition~~ provisions of FASB Statement No. 123(R), “Share-Based Payment~~” (“Statement 123(R)”), using the modified-prospective-transition method~~.

~~Under~~ The ~~the~~fair ~~modified-prospective-transition~~value ~~method,~~of ~~compensation~~each ~~cost~~option ~~recognized~~grant inis estimated on the ~~second quarter~~date of ~~fiscal~~grant ~~2006~~using ~~includes:~~the ~~(a) compensation~~Black-Scholes option-pricing ~~cost~~model ~~for~~and ~~all~~recognized ~~share-based~~as ~~payments~~compensation ~~granted~~expense ~~prior to~~over ~~but~~the ~~not~~vesting ~~yet~~period ~~vested as~~ of ~~January 1,~~the ~~2006,~~award using ~~based~~the onaccelerated ~~the~~attribution ~~grant~~method. ~~date~~There ~~fair value~~were ~~estimated~~no inoptions ~~accordance~~granted ~~with~~during the ~~original~~three ~~provisions~~months ended ~~of Statement 123~~March 31, ~~and~~2009. ~~(b) compensation cost~~The ~~for~~following ~~all share~~weighted-~~based~~average ~~payments~~assumptions ~~granted~~were ~~subsequent~~used tofor ~~January 1,~~options ~~2006,~~granted during ~~based on~~ the ~~grant-date fair~~three ~~value~~months ~~estimated~~ended inMarch 31, ~~accordance~~2008, ~~with~~and ~~the~~a ~~provisions~~discussion of ~~Statement~~the ~~123(R).~~Company’s ~~Results~~methodology for ~~prior~~ ~~periods~~developing ~~have~~each ~~not been restated. The adoption~~ of ~~Statement~~the ~~123(R)~~assumptions ~~has~~used noin ~~impact on~~ the ~~cash~~valuation ~~flows from~~model ~~operating or financing activities.~~follows:

The following table illustrates the effect on net loss and net loss per share if the Company had applied the fair value recognition provisions of Statement 123(R) to stock-based employee compensation for the three- and six-month periods ended June 30, 2005. The reported and pro forma net loss and net loss per share for the three- and six-month periods ended June 30, 2006 are the same because stock-based compensation expense is calculated under the provisions of Statement 123(R). The amounts for the three-month period ended June 30, 2006 are included in the table below only to provide net loss and net loss per share for a comparative presentation to the period of the previous year.


	Three Months		Three Months
	Ended		Ended
	March 31,		March 31
	2009		2008
Dividend yield		—		0.00	%
Expected volatility		—		68.2	%
Risk-free interest rate		—		3.59	%
Expected life of the option term (in years)		—		6.8
Forfeiture rate		—		4.20	%

	Three months ended						Six months ended
	June 30,						June 30,
(in thousands, except per share data)	2006			2005			2006			2005
Net loss, as reported	$	(4,429	)	$	(4,349	)	$	(8,987	)	$	(13,421	)
Add: Stock-based non-employee compensation expense included in reported net loss	$	—		$	92		$	—		$	93
Deduct: Stock-based employee compensation expense if SFAS No. 123 had been applied to all grants	$	—		$	(46	)	$	—		$	(68	)
Pro forma net loss	$	(4,429	)	$	(4,303	)	$	(8,987	)	$	(13,396	)
Net loss per share:
Basic and diluted — as reported	$	(0.44	)	$	(33.56	)	$	(0.94	)	$	(103.92	)
Basic and diluted — pro forma	$	(0.44	)	$	(33.20	)	$	(0.94	)	$	(103.73	)

Dividend Yield— The Company has never declared or paid dividends and has no plans to do so in the foreseeable future.

~~Pro~~Expected ~~forma~~Volatility— ~~information~~Volatility ~~regarding~~is ~~net~~a ~~loss~~measure ~~and~~of ~~net~~the ~~loss~~amount ~~per share is required~~ by ~~Statement~~ ~~123~~which ~~and,~~a infinancial ~~periods~~variable ~~prior~~such ~~to January 1, 2006, had been determined~~ as ifa share ~~the~~price ~~Company~~ has ~~accounted~~ ~~for~~fluctuated ~~its~~(historical ~~employee~~volatility) ~~stock~~or ~~options~~is ~~under~~expected ~~the~~to ~~fair~~fluctuate ~~value~~(expected volatility) ~~method~~during a period. The ~~fair~~Company ~~value~~uses ofan ~~each option~~average ~~grant~~of ~~is estimated on~~ the ~~date~~volatility of ~~grant~~its ~~using~~own ~~the~~stock ~~Black-Scholes~~and ~~option-pricing fair value~~the ~~model. The following weighted-~~average ~~assumptions~~volatility ~~were used for options granted in three and six months ended June 30, 2006 and a discussion~~ of ~~our~~similar ~~methodology~~companies ~~for developing each of the assumptions used~~ in the ~~valuation~~pharmaceutical ~~model follows:~~industry.

	Three Months Ended			Six Months Ended
	June 30, 2006			June 30, 2006
Dividend yield		0.00	%		0.00	%
Expected volatility		67.30	%		66.32	%
Risk-free interest rate		4.86	%		4.71	%
Expected life of the option term (in years)		6.0			6.0
Forfeiture rate		2.68	%		2.68	%

Risk-Free Interest Rate— This is the U.S. Treasury rate for the week of each option grant during the quarter having a term that most closely resembles the expected life of the option term.

~~Dividend~~Expected ~~Yield~~Life of the Option Term—~~The~~ ~~Company~~This ~~has~~is ~~never~~the ~~declared~~period orof ~~paid~~time ~~dividends~~that ~~and~~the ~~has~~options nogranted ~~plans~~are expected to doremain sounexercised. inThe expected term is based upon management’s consideration of the historical ~~foreseeable~~life ~~future~~of options, the vesting period of the option granted and the contractual period of the option granted.

~~Expected~~Forfeiture ~~Volatility~~Rate—~~Volatility~~ This is ~~a measure of~~ the ~~amount~~estimated bynumber ~~which~~of astock ~~financial~~options ~~variable~~granted ~~such~~that asare ~~a share price has fluctuated (historical volatility) or is~~ expected to ~~fluctuate (expected~~be ~~volatility)~~forfeited ~~during~~or acancelled ~~period.~~on ~~Due~~an toannual ~~the~~basis ~~Company’s~~before ~~limited~~becoming ~~trading~~fully ~~history, there is inadequate data to calculate historical volatility of our stock~~vested. The Company ~~has~~estimates ~~used an average volatility of similar companies in~~ the ~~pharmaceutical industry. This volatility has averaged 67.3%, with a~~ ~~high~~forfeiture ~~and~~rate ~~low~~based ~~value~~on ofpast ~~94.0%~~turnover ~~and 42%, respectively~~data.

~~Risk-Free Interest Rate—This is the U.S. Treasury rate for the week of each option grant during the~~7 ~~quarter having a term that most~~

Page 6

closely resembles the term of the option.

Expected Life of the Option Term—This is the period of time that the options granted are expected to remain unexercised. Options granted during the quarter have a maximum term of ten years. The Company has adopted SAB 107’s simplified method for estimating the expected term of stock options.

Forfeiture Rate—This is the estimated number of stock options granted that are expected to be forfeited or cancelled on an annual basis before becoming fully vested. The Company estimates the forfeiture rate based on past turnover data.

The Company accounts for equity instruments issued to non-employees in accordance with Emerging Issues Task Force 96-18, “Accounting for Equity Instruments that are Issued to other than Employees for Acquiring, or in Conjunction with Selling, Goods, or Services”. For the six months ended June 30, 2006, compensation expense of $9,000 was recognized for the issuance of stock and stock options to non-employees.

Stock Compensation Plans

The Company adopted the Avalon Pharmaceuticals, Inc. 1999 Stock Incentive Plan (the “1999 Plan”) to provide for the granting of stock awards, such as stock options, restricted common stock, and stock appreciation rights to employees, directors and other individuals as determined by the Board of Directors. The Company ~~has~~terminated the 1999 Plan as to future awards effective upon the closing of the Company’s initial public offering in October 2005. As of March 31, 2009, the Company had reserved ~~624~~338,~~143~~335 shares of common stock to accommodate the exercise of ~~options~~outstanding options granted under the 1999 Plan.

~~The~~ Effective upon the closing of the Company’s ~~terminated~~initial public offering in October 2005, the Company ~~1999~~adopted the Avalon Pharmaceuticals, Inc. 2005 Omnibus Long-Term Incentive Plan as(the “2005 Plan”) to ~~future~~provide for the granting of stock awards, ~~effective~~such ~~upon~~as stock options, restricted common stock, stock units, dividend equivalent rights, stock appreciation rights and unrestricted common stock, and other performance and annual incentive awards to employees, directors and other individuals as determined by the ~~closing~~Board of Directors. At the inception of the 2005 Plan, 989,738 shares were ~~Company’s~~reserved ~~initial~~for ~~public~~issuance ~~offering~~under the 2005 Plan. The number of shares available for issuance under the 2005 Plan was increased from 989,738 shares to 1,581,582 shares in ~~October~~June 2006 and from 1,581,582 shares to 2,381,582 shares in June 2007. Additionally, shares that become available due to forfeiture of outstanding awards under the 1999 Plan are available for awards under the 2005 Plan. As of March 31, 2009, the Company had reserved 1,397,280 shares of common stock to accommodate the exercise of outstanding option grants under the 2005 Plan and had reserved 1,143,589 shares of common stock for future grants under the 2005 Plan.

Effective upon the closing of the Company’s initial public offering in October 2005, the Company adopted the Avalon Pharmaceuticals, Inc. 2005 Omnibus Long-Term Incentive Plan (the “2005 Plan”) to provide for the granting of stock awards, such as stock options, restricted common stock, stock units, dividend equivalent rights, stock appreciation rights and unrestricted common stock, and other performance and annual incentive awards to employees, directors and other individuals as determined by the Board of Directors. The Company reserved 989,738 shares of common stock to accommodate the exercise of options granted under the 2005 Plan.

In June 2006, the 2005 Plan was amended and restated to increase the number of shares of Common Stock available for grants and awards under the 2005 Plan by 591,844 shares to a total of 1,581,582 shares.

Generally, stock options are granted with an exercise price that equals the fair market value of the Company’s common stock on the grant date. Options typically have a life of ten years and vest over periods ranging from six months to five years. Options generally expire 90 days after an employee terminates employment with the Company.

~~Shares~~ The oftotal ~~common~~fair ~~stock~~value ~~issued to non-employee directors, as part~~ of ~~their~~stock ~~annual~~options ~~director compensation,~~which ~~for~~vested during the three- ~~and six-~~month ~~periods~~period ended ~~June~~March 3031, 2009 ~~2006~~was ~~were~~approximately 5$92,~~544~~000. ~~and~~There 11were 1,~~471~~463, ~~respectively.~~937 ~~The~~fully ~~fair~~vested ~~market~~stock ~~value~~options ofoutstanding ~~these shares~~at March 31, on2009. ~~the~~These ~~date~~stock ofoptions ~~grant,~~had ~~was~~a ~~approximately $27,000~~weighted ~~and~~average ~~$54,900,~~remaining ~~respectively~~life of 6.15 years.

The total intrinsic value of stock options exercised during the three- and six-month periods ended June 30, 2006 was approximately $11,000 and $40,000, respectively. The weighted-average grant-date fair value of equity awards granted during the three- and six-month periods ended June 30, 2006 was $2.94 and $2.89, respectively. The total fair value of stock options which vested during the three- and six-month periods ended June 30, 2006 was approximately $360,000 and $1.2 million, respectively. There were 927,017 fully vested stock options outstanding at June 30, 2006. These stock options had a weighted average remaining life of 6.99 years.


					Weighted-
			Weighted-		Average		Aggregate
			Average		Remaining		Intrinsic
			Exercise		Contractual		Value
	Shares		Price		Term		(in thousands)
Outstanding at December 31, 2008		2,231,957	$	3.44
Granted		—		—
Exercised		—		—
Forfeited or expired		496,342		1.58


Outstanding at March 31, 2009		1,735,615		3.97


Vested and expected to vest at March 31, 2009		1,673,129	$	4.07		6.15	$	—
Exercisable at March 31, 2009		1,463,937	$	4.07		6.15	$	—

						Weighted-
				Weighted-		Average
				Average		Remaining		Aggregate
				Exercise		Contractual		Intrinsic Value
	Shares			Price		Term		(in thousands)
Outstanding at April 1, 2006		1,265,341		$	4.62
Granted		15,950			4.54
Exercised		(4,513	)		1.78
Forfeited or expired		(25,951	)		4.55
Outstanding at June 30, 2006		1,250,827		$	4.63		7.58	$	259
Vested and expected to vest at June 30, 2006		927,017		$	4.36		6.99	$	254
Exercisable at June 30, 2006		927,017		$	4.36		6.99	$	254

No stock options were granted or exercised during the three months ended March 31, 2009. Due to the valuation allowance on all deferred tax assets, the Company recorded no tax benefit for stock compensation expense recognized during the three months ended March 31, 2009. As of March 31, 2009, unamortized stock-based compensation expenses of approximately $190,000 remains to be recognized over a weighted average period of 2.2 years.

~~Cash received from the exercise of stock options under all share-based payment arrangements for the three months ended June 30, 2006 was $~~8~~,000. Due to the valuation allowance on all~~ deferred tax assets, the Company recorded no tax benefit for options exercised during the three months ended June 30, 2006. As of June 30, 2006, there was approximately $669,000 of total unrecognized compensation costs related to nonvested employee stock options. That cost is expected to be recognized over a weighted average period of 2.94 years.

Page 7

Basic and Diluted Net Loss Attributable to Common Stockholders Per Common Share

Basic net loss attributable to common stockholders per common share excludes dilution for potential common stock issuances and is computed by dividing net loss ~~attributable to common stockholders~~ by the weighted-average number of common shares outstanding for the period. Diluted net loss ~~attributable to common stockholders~~ per common share reflects the potential dilution that could occur if securities or other contracts to issue common stock were exercised or converted into common stock. ~~Mandatorily~~Stock ~~redeemable convertible preferred stock, stock~~ options, and warrants were not considered in the computation of diluted net loss ~~attributable~~per to common ~~stockholders per common~~ share for the periods presented, as their effect is antidilutive.

37. ~~Common~~Fair ~~Stock~~Value Measurements

In ~~February~~September 2006, the ~~Company~~FASB ~~raised~~issued $7SFAS No.25 ~~million~~157, ~~through~~Fair aValue ~~private~~Measurements ~~placement~~(“SFAS of157”). ~~1,666,666~~SFAS 157 ~~shares~~provides ofguidance ~~its~~for ~~common~~using ~~stock~~fair value to ~~nine~~measure ~~institutional~~assets ~~investors~~and liabilities. ~~The~~It ~~proceeds~~also ~~from~~responds ~~this~~to investors’ ~~financing~~requests ~~will~~for expanded information about the extent to which companies measure assets and beliabilities at fair value, the information used to ~~expand~~measure fair value and the ~~Company’s~~effect ~~internal~~of ~~oncology~~fair ~~drug~~value measurements ~~discovery~~on ~~programs~~earnings. ~~Offering~~SFAS ~~expenses~~157 applies whenever other standards require (or permit) assets or liabilities to be measured at fair value, and does not expand the use of fair value in any new ~~$70~~circumstances. SFAS 157 establishes a three-tier fair value hierarchy,~~000~~ ~~were~~which ~~recorded~~prioritizes tothe ~~additional~~inputs used ~~capital~~in measuring fair value. These tiers include:

4.• ~~Related~~Level ~~Party~~1, ~~Transactions~~ defined as observable inputs such as quoted prices in active markets for identical assets; • Level 2, defined as observable inputs other than level 1 prices such as quoted prices for similar assets; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities; and • Level 3, defined as unobservable inputs in which little or no market data exists, therefore requiring an entity to develop its own assumptions.

The Company’s ~~paid~~cash ~~two~~equivalents ~~members~~are ofsubject ~~the~~to ~~board~~fair ofvalue ~~directors~~measurements. ~~consulting~~The ~~fees~~inputs ~~totaling~~used ~~$62,100~~in ~~and~~measuring ~~$65,850~~the ~~for~~fair ~~the~~value ~~six~~of ~~months~~these ~~ended~~instruments ~~June 30,~~are ~~2006~~considered ~~and~~to ~~2005,~~be ~~respectively~~level 1 in accordance with the SFAS 157 hierarchy.

On December 1, 2005, Avalon entered into a contract to lease certain unused equipment to NeoDiagnostix upon the approval of the transaction by independent members of the Company’s board of directors8. ~~Kenneth~~Related C.Party ~~Carter, Ph.D., the Company’s President, Chief Executive Officer and~~Transactions ~~Director, is a director and minority shareholder in NeoDiagnostix, a privately held company focused on providing oncology diagnostic testing on a fee-for-service basis.~~

5. The ~~Income~~Company ~~Taxes~~paid one member of the board of directors consulting fees totaling $14,000 for the three months ended March 31, 2009.

~~For the three- and six-month periods ended June 30, 2006, there is no current provision for income taxes and the deferred tax benefit has been entirely offset by valuation allowances~~9. ~~The difference~~Income ~~between the amounts of income tax benefit that would result from applying domestic~~Taxes ~~federal statutory income tax rates to the net loss and the net deferred tax assets is related to certain nondeductible expenses, state income taxes, and the change in the valuation allowance.~~

6 For the three month periods ended March 31, 2009, and 2008, there is no current provision for income taxes and the deferred tax benefit has been entirely offset by valuation allowances. ~~Debt~~The difference between the amounts of income tax benefit that would result from applying domestic federal statutory income tax rates to the net loss and the net deferred tax assets is related to certain nondeductible expenses, state income taxes, and the change in the valuation allowance.

In August 2005, the Company entered into a modification agreement with MIDFA and M&T Bank under its letter of credit agreement pursuant to which M&T Bank agreed to waive the Company’s compliance with all financial covenants contained in the Company’s letter of credit with M&T Bank guaranteeing the Company’s development bond financing obligations to MIDFA10. ~~The~~Subsequent ~~minimum tangible~~Event net worth, minimum restricted cash balance and minimum ratio of current assets to current liabilities financial covenants were waived until April 1, 2006. In exchange for this waiver, the Company increased by $500,000 the cash collateral amount held as restricted cash under the letter of credit to approximately $6.3 million. On April 1, 2006 the waivers expired and the cash collateral amount held as restricted cash was reduced to approximately $5.5 million. The Company is in compliance with all financial covenants contained in the Company’s letter of credit.

~~Page~~ Effective 8May 1, 2009, Avalon and Merck & Co., Inc. (“Merck”) agreed to terminate the Exclusive License and Research Collaboration Agreement between the parties (the “Merck Agreement”) pursuant to the terms of the Merck Agreement. As part of the termination of the Merck Agreement, Merck agreed to pay the Company a termination payment of $4 million. The $4 million termination payment was paid by Merck to Avalon on May 7, 2009. The Company will recognize the termination payment as revenue in the second quarter of 2009.

Under the terms of the Merger Agreement with Clinical Data, the $4 million payment received by Avalon from Merck is required to be used to pay down the outstanding balance, including interest, of the Secured Loan. See Note 3 above. As of April 30, 2009, a total of approximately $4.1 million in principal and accrued interest remained outstanding under the Secured Loan. On May 8, 2009, Avalon paid Clinical Data a total of $4 million in respect of the Secured Loan, reducing the outstanding balance of the Secured Loan by that amount.

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis of our results of operations, financial condition ~~and~~ and liquidity and capital resources should be read in conjunction with our unaudited consolidated financial statements and related notes contained in this Quarterly Report on Form 10-Q , as well as the audited financial statements and related notes for the fiscal year ended December 31, ~~2005~~2008 and “Management’s Discussion and Analysis of Financial Condition and Results of Operations,” contained in our Annual Report on Form 10-K , for the fiscal year ended December 31, ~~2005~~2008.

Overview

We are a biopharmaceutical company focused on the discovery, ~~and~~ development ~~of small molecule~~and ~~therapeutics.~~commercialization ~~Our pipeline~~ of ~~drug~~first-in-class ~~candidates~~cancer ~~includes~~therapeutics. ~~our~~We ~~lead~~use AvalonRx ~~candidate~~®, ~~AVN944.~~our ~~AVN944 is an~~proprietary ~~oral~~platform, ~~small~~which ~~molecule~~is ~~drug~~based ~~candidate~~on ~~that~~large-scale ~~was~~biomarker ~~discovered~~identification ~~by Vertex Pharmaceuticals Incorporated~~ and ~~that~~ wemonitoring, ~~licensed from Vertex in February 2005. AVN944 is currently in early stage clinical development for the treatment of hematological cancers. We seek~~ to discover and develop ~~novel~~ therapeutics ~~through~~for ~~the~~pathways ~~use~~that ofhave ahistorically ~~comprehensive,~~been ~~innovative~~characterized ~~and~~as ~~proprietary suite of technologies based upon large-scale gene expression analysis, which we call AvalonRx®~~“undruggable.”

Since weour ~~commenced business in January 2000~~inception, our operations have consisted primarily of developing AvalonRx ®, utilizing our technology to seek to discover and develop novel cancer therapeutics, and the in-license and ~~subsequent~~ development of AVN944. InDuring that period, we have generated limited revenue from collaborative partners, and have had no revenue from product sales. Our operations have been funded principally through the offering of equity securities and debt financings.

We have never been profitable and, as of ~~June~~March 3031, ~~2006~~2009, we had an accumulated deficit of $94149.6 8 million. We had net losses of $93.06 million for the ~~six~~three months ended ~~June~~March 3031, ~~2006~~2009 and net losses of $1921.38 million for the year ended December 31, ~~2005~~2008. We expect to incur significant ~~and increasing~~ operating losses for the foreseeable future as we advance our drug candidates from discovery through preclinical testing and clinical trials and seek regulatory approval and eventual commercialization. ~~In addition to these increasing research and development expenses, we expect general and administrative costs to increase as we add personnel.~~ We will need to generate significant revenues to achieve profitability, and we may never do so.

~~Financial~~ As ~~Operations~~of ~~Overview~~March 31, 2009, we had cash, cash equivalents and marketable securities of ~~Revenue~~approximately $3.5 million. We currently estimate that our existing capital resources will not be sufficient to fund our current operations significantly beyond the end of May 2009, by which time our pending merger with a subsidiary of Clinical Data is expected to close. If our proposed merger does not close by the end of May 2009, we would need to raise additional funds to continue operations. See “—Recent Developments” below. In light of the proposed merger, we do not expect to seek to raise additional capital. Should the merger not close or if the closing is delayed beyond the end of May 2009, there is no assurance that we would be able to raise capital sufficient to enable us to continue our operations significantly beyond the end of May 2009. In the event we were unable to successfully raise additional capital in such circumstances, we will not have sufficient cash flows and liquidity to finance our business operations as currently contemplated. Accordingly, in such circumstances we would be compelled to reduce general and administrative expenses and delay research and development projects and the purchase of scientific equipment and supplies until we were able to obtain sufficient financing.

Pending Acquisition by Clinical Data

On October 27, 2008, Avalon entered into a merger agreement with Clinical Data, Inc., or Clinical Data, and API Acquisition Sub II, LLC, an indirect wholly-owned subsidiary of Clinical Data, or API. The merger agreement provides that, upon the terms and subject to the conditions set forth in the merger agreement, API will be merged with and into Avalon, with Avalon continuing as the surviving corporation and a subsidiary of Clinical Data. In connection with entering into the merger agreement with Clinical Data, Avalon borrowed $4 million from Clinical Data under a note purchase agreement with Clinical Data, to fund Avalon’s short-term on-going operations, entered into a license agreement with Clinical Data under which Clinical Data received an exclusive license (subject to certain exceptions) to AvalonRx^® in exchange for a one time license fee of $1 million, and engaged in a private placement with Clinical Data of Avalon common stock and warrants for a cash payment of $237,338 from Clinical Data.

Recent Developments

Effective May 1, 2009, Avalon and Merck & Co., Inc., or Merck, agreed to terminate the Exclusive License and Research Collaboration Agreement between the parties (referred to as the “Merck Agreement”) pursuant to the terms of the Merck Agreement. As part of the termination of the Merck Agreement, Merck agreed to pay Avalon a termination payment of $4 million. The $4 million termination payment was paid by Merck to Avalon on May 7, 2009. Avalon will recognize the termination payment as revenue in the second quarter of 2009.

Under the terms of the merger agreement with Clinical Data, the $4 million payment received by Avalon from Merck was required to be used to pay down the outstanding balance, including interest, of our secured loan with Clinical Data. See “—Liquidity and Capital Resources—Clinical Data Secured Loan” below. As of April 30, 2009, a total of approximately $4.1 million in principal and accrued interest remained outstanding under this secured loan. On May 8, 2009, Avalon paid Clinical Data a total of $4 million in respect of the secured loan, reducing the outstanding balance of the secured loan by that amount.

Financial Operations Overview

Revenue

We have not generated any revenue from sales of commercial products and do not expect to generate any product revenue for the foreseeable future. To date, our revenue has consisted of collaboration revenue.

Collaboration Revenue. Since inception, we have generated revenue solely in connection ~~with~~ with our collaboration and pilot study agreements. Our collaborations with ~~MedImmune~~Merck, ~~and~~AstraZeneca ~~Novartis~~and Novartis include upfront payments, research funding, and/or payments for the achievement of certain ~~discovery~~ discovery and development related milestones. During the ~~third~~first ~~quarter~~three months of ~~2005~~2009, we ~~began~~recognized no ~~to recognize~~ revenue ~~under~~ ~~our~~from ~~collaboration~~any ~~with MedImmune which was signed in June 2005. As~~ of ~~June 30, 2006, we have not recognized any revenue under~~ our ~~collaboration with Novartis~~collaborations.

Research and Development Expense

Research and development expense consists of expenses incurred in connection with ~~developing~~ developing and advancing our drug discovery technology and identifying and developing our drug candidates and supporting our collaborative relationships. These expenses consist primarily of salaries and related expenses, the purchase of laboratory supplies, access to data sources, facility costs, costs for preclinical development and expenses related to our in-license and clinical trials of AVN944. WeOther than for advance payments for research and development costs, subject to the provisions of EITF 07-03, we charge all research and development expenses to ~~operations~~ operations as incurred.

We expect our research and development costs to be substantial ~~and to increase~~ as we advance ~~AVN944~~ ~~through~~our ~~clinical trials and move other~~ drug candidates into preclinical testing and clinical trials. Based on the results of our preclinical studies, we expect to selectively advance some drug candidates into clinical trials. We anticipate that we will select drug candidates and research projects for further development on an ongoing basis in response to their preclinical and clinical success and commercial potential. ~~With~~We ~~regard~~are currently toconducting Phase I clinical trials for AVN944, wein ~~initiated~~patients ~~U.S.~~with hematological cancer and Phase IIIa clinical trials for patients with pancreatic cancer. In August 2008, we announced that we had reached a likely maximum tolerated dose of AVN944 in ~~cancer~~both ~~patients~~the ongoing Phase I clinical trial and in ~~January 2006~~the Phase IIa trial. We are currently assessing various alternatives regarding the internal or external development of AVN944.

General and Administrative

General and administrative expense consists primarily of salaries and related expenses ~~for~~ for personnel in administrative, finance, business development and human resource functions. Other costs include legal costs of pursuing patent protection of our intellectual property, ~~unallocated facility costs~~ and ~~professional~~other fees for legal services. ~~We anticipate increases in general and~~ administrative expense relating to operating as a public company. These increases will likely include legal fees, accounting fees and directors’ and officers’ insurance premiums as well as fees for investor relations services.

~~Critical Accounting Policies and Significant Judgments and Estimates~~11

Stock-Based Compensation

In December 2004, the Financial Accounting Standards Board (“FASB”) issued Statement of Financial Accounting Standards (“SFAS”) No. 123, revised 2004, or SFAS 123(R), “Share-Based Payment ” SFAS 123(R) supersedes Accounting Principles Board (“APB”) Opinion No. 25, “Accounting for Stock Issued to Employees ” (“APB 25”), and requires companies to recognize compensation expense, using a fair-value based method, for costs related to share-based payments, including those made pursuant to stock option and employee stock purchase plans.

We adopted SFAS 123(R) on January 1, 2006 using the modified prospective transition method, which requires that stock-based compensation cost is recognized for all awards granted, modified or settled after the effective date as well as for all awards granted to employees prior to the effective date that remain unvested as of the effective date. Prior to the adoption, we disclosed such costs on a pro forma basis in the notes to our financial statements. In accordance with the modified prospective method, the financial statements for prior periods have not been restated to reflect the impact of FAS 123R.

Page 9

For and six months ended June 30, 2006, we recorded approximately $1.2 million of stock-based compensation expenses, of which $367,000 was included in research and development expense and $861,000 was included in general and administrative expense. Since we continue to operate in a net loss, the adoption of SFAS 123(R) had no impact for tax-related effects on cash flow from operations and cash flow from financing activities for the six months ended June 30, 2006. As of June 30, 2006, unamortized stock-based compensation expenses of approximately $669,000 remains to be recognized over a weighted-average period of approximately 3 years. We amortize stock-based compensation expenses on a straight-line ratable basis over the vesting period.

We estimated the fair value of stock options granted during the three months ended June 30, 2006 using the Black-Scholes option pricing model. The assumptions used under this model are as follows: (i) expected term of 6 years based on the simplified method for estimating the expected term of stock options; (ii) expected volatility of 67.3% based on historical and peer volatility data; (iii) weighted average risk-free interest rate of 4.86% based on the U.S. Treasury yield curve in effect at the time of grant for periods corresponding with the expected term of the option; and (iv) expected dividend yield of zero percent. In addition, under SFAS 123(R), the fair value of stock options granted is recognized as expense over the service period, net of estimated forfeitures. Based on historical data, we calculated a 2.68% annual forfeiture rate, which we believe is a reasonable assumption. However, the estimation of forfeitures requires judgment, and to the extent actual results or updated estimates differ from our current estimates, such amounts will be recorded as a cumulative adjustment in the period estimates are revised.

The Black-Scholes option pricing model requires the input of highly subjective assumptions. Because our employee stock options have characteristics significantly different from those of traded options, and because changes in the subjective input assumptions can materially affect the fair value estimate, in management’s opinion, the existing models may not provide a reliable single measure of the fair value of our employee stock. In addition, management will continue to assess the assumptions and methodologies used to calculate estimated fair value of share-based compensation. Circumstances may change and additional data may become available over time, which result in changes to these assumptions and methodologies, and which could materially impact our fair value determination.

Results of Operations

Three Months Ended ~~June~~March 3031, ~~2006~~2009 and ~~2005~~2008

Revenue. ~~Total~~There ~~revenues~~were ~~increased~~no torevenues ~~$417,000,~~ for the three months ended ~~June~~March 3031, ~~2006~~2009, compared ~~to no revenue for the three months ended June 30, 2005. This revenue was primarily attributable to MedImmune~~ with ~~a small portion of revenue attributable to our collaboration~~ ~~agreement with the University of Louisville. Following a review of our collaboration agreements, we have determined that we prematurely recorded an aggregate of~~ $~~535~~50,000 ~~of revenue~~ in ~~prior quarters~~the ~~under~~same ~~our~~period ~~agreement~~of ~~with~~the ~~MedImmune~~prior year. AnThe ~~adjustment~~reported torevenues ~~reduce revenue by $535,000 was made~~ in ~~the~~2008 ~~second~~were ~~quarter~~attributable ~~of 2006~~ to ~~reflect properly total revenue recorded through June 30, 2006~~ ~~under~~our ~~this~~collaboration agreement. ~~This~~with ~~adjustment had no impact on cash received from MedImmune under the terms of the agreement~~Novartis.

Research and Development. Research and development expenses ~~increased~~decreased by $~~717~~1.7 million,~~000,~~ or 2739%, to $32.37 million for the three months ended ~~June~~March 3031, ~~2006~~2009 from $24.64 million for the same period in ~~2005~~ 2007. The ~~increase~~decrease in research and development expenses was primarily attributable to ~~compensation expense related to the issuance of stock options, an~~ ~~increase~~lower inpersonnel ~~outside~~and ~~services~~lab supplies costs ~~related~~due to ~~our~~the ~~AVN944~~reduction ~~drug~~in ~~candidate~~force ~~and~~in anAugust 2008 ~~increase~~as inwell ~~lab~~as ~~supplies~~lower ~~expense~~cost ~~related,~~for inclinical ~~part,~~trials toin ~~our~~the ~~collaboration~~2009 ~~agreement with MedImmune~~period.

~~Research~~ General and ~~development~~Administrative. ~~expenses~~General ~~consist~~and ofadministrative ~~direct~~expenses ~~costs~~decreased ~~which~~by ~~include~~$1.2 million ~~salaries~~or ~~and~~57% ~~related costs~~when ofcomparing ~~research~~the ~~and~~three ~~development~~months ~~personnel~~ended March 31, ~~and~~2009 with the ~~costs~~three ofmonths ~~consultants~~ended March 31, ~~materials~~2008. ~~and~~The ~~supplies associated~~decrease ~~with~~is ~~research~~due ~~and~~primarily ~~development~~to ~~projects.~~lower ~~Indirect~~personnel ~~research~~costs ~~and~~due ~~development~~to ~~costs~~the ~~include~~reduction in ~~facilities,~~force ~~depreciation,~~in ~~patents~~August 2008 ~~and~~as ~~other~~well ~~indirect~~as ~~overhead~~lower ~~costs~~stock compensation expense in 2009.

~~During~~ Interest Income. There was no interest income for the ~~remainder~~three ofmonths ~~2006~~ended March 31, ~~and~~2009, compared ~~thereafter~~with $307,000 ~~research~~for ~~and~~the ~~development~~three ~~expenses~~months ~~will~~ended ~~increase~~March 31, 2008. The decrease in interest income ~~substantially~~is asdue weto ~~continue~~lower ~~Phase~~balances Iof ~~clinical~~cash ~~studies~~and ~~for~~investments ~~our~~and ~~AVN944~~lower ~~drug~~average ~~candidate~~interest rates.

~~General~~ Interest ~~and Administrative~~Expense. ~~General~~Interest ~~and~~expense ~~administrative~~decreased ~~expenses increased~~ by $~~510~~63,000, or ~~40%~~ 55%, to $~~1.8 million~~52,000 for the three months ended ~~June~~March 3031, ~~2006~~2009, compared to $~~1.3 million~~115,000 for the three months ended ~~June~~March 3031, ~~2005~~2008. The ~~increase~~decrease isin ~~attributable~~interest expense was due to ~~compensation~~lower ~~expense~~debt ~~related~~balances toin the ~~issuance~~ of2009 ~~stock options~~period, ~~accrued~~principally related ~~bonuses~~to ~~for~~paying ~~executives~~off ~~and~~our ~~staff,~~loan ~~and~~the ~~other~~Maryland ~~expenses~~Industrial ~~from operating~~Development asFinancing aAuthority ~~public~~in ~~company~~October 2008.

~~Interest~~ Other Income. ~~Interest~~Other income ~~increased~~was by $~~252~~80,000 ~~or 304%, to $335,000~~ for the three months ended ~~June~~March 3031, ~~2006~~2009, compared towith $832,000 for the three months ended ~~June~~March 3031, ~~2006~~2008. The increase in ~~interest~~other income iswas primarily arelated ~~result~~to ofincome ~~interest earned on proceeds~~ from ~~issuance~~subletting part of ~~common stock, including proceeds from~~ our ~~initial~~facility ~~public~~and ~~offering,~~the ~~and~~provision ~~higher~~of ~~average~~shared services ~~interest~~to ~~rates~~subtenants.

Interest Expense. Interest expense decreased by $109,000, or 34%, to $204,000 for the three months ended June 30, 2006, compared to $313,000 for the three months ended June 30, 2005. The decrease in interest expense was primarily related to the conversion of our outstanding convertible notes into common stock at the close of our initial public offering in October 2005, and lower balances on our long term debt. This decrease was offset, in part, by higher average interest rates on our long term debt and development bond financing.

Other Income. Other income was $156,000 for the three months ended June 30, 2006, compared to $157,000 for the three months ended June 30, 2005. All of our other income during the period consisted of income from subletting part of our facility and the provision of shared services to our subtenants.

Six Months Ended June 30, 2006 and 2005

Revenue. Total revenues increased to $956,000, for the six months ended June 30, 2006, compared to $0 for the six months ended June 30, 2005. Substantially all 2006 revenues are related to our collaboration agreement with MedImmune, Inc. A small portion of revenue was attributable to our collaboration agreement with the University of Louisville. Following a review of our collaboration agreements, we have determined that we prematurely recorded an aggregate of $535,000 of revenue in prior quarters under our agreement with MedImmune. An adjustment to reduce revenue by $535,000 was made in the second quarter of 2006 to reflect properly total revenue recorded through June 30, 2006 under this agreement. This adjustment had no impact on cash received from MedImmune under the terms of the agreement.

Page 10

We expect that collaborative research and development revenues will continue to be a significant source of our total revenue and entered into an additional collaboration agreement with Novartis Institutes for Biomedical Research, Inc. during the third quarter of 2005 that could be material to our business. No revenue was recognized under the Novartis agreement during the quarter.

Research and Development. Research and development expenses decreased $3.5 million, or 35%, to $6.5 million for the six months ended June 30, 2006 from $10.0 million for the same period in 2005. The decrease in research and development expenses was primarily attributable to the inclusion in the prior year period of an upfront payment of $5.0 million to Vertex for the in-license of AVN944. This decrease was offset by compensation expense related to the issuance of stock options, an increase in outside services costs related to our AVN944 drug candidate and an increase in lab supplies expense related, in part, to our collaboration agreement with MedImmune.

General and Administrative. General and administrative expenses increased by $1.6 million or 65%, to $4.0 million for the six months ended June 30, 2006 compared to $2.5 million for the six months ended June 30, 2005. The increase was primarily attributable to compensation expense related to the issuance of stock options, accrued bonuses for executives and staff, new hires and salary increases, increase in franchise taxes and other expenses directly related to operating as a public company. These increases were offset, in part, by a decrease in professional fees and other outside services expenses for the six months ended June 30, 2006.

Interest Income. Interest income increased by $508,000, or 313%, to $670,000 for the six months ended June 30, 2006 compared to $163,000 for the six months ended June 30, 2005. The increase in interest income is a result of interest earned on proceeds from issuance of common stock, including proceeds from our initial public offering, and higher average interest rates.

Interest Expense. Interest expense decreased by $177,000, or 29%, to $424,000 for the six months ended June 30, 2006 compared to $602,000 for the six months ended June 30, 2005. The decrease in interest expense was primarily related to the conversion of our outstanding convertible notes into common stock at the close of our initial public offering in October 2005 and lower balances on our long term debt. This decrease was offset, in part, by higher average interest rates on our long term debt and development bond financing.

Other Income. Other income increased by $124,000, or 55%, to $346,000 for the six months ended June 30, 2006 compared to $222,000 for the six months ended June 30, 2005. All other income during the period consisted of income from subletting part of our facility and the provision of shared services to our subtenants.

Liquidity and Capital Resources

Our primary cash requirements are to:

• fund our research and development and clinical programs; • obtain regulatory approvals; • prosecute, defend and enforce any patent claims and other intellectual property rights; • fund general corporate overhead; and • support our debt service requirements and contractual obligations.

Our cash requirements could change materially as a result of the progress of our research and development and clinical programs, licensing activities, acquisitions, divestitures or other corporate developments.

We have incurred operating losses since our inception and historically have financed our operations principally through public stock offerings, debt financings, private ~~placement~~placements of equity securities, strategic collaborative agreements that include research and development funding, and development milestones, and investment income.

In evaluating alternative sources of financing we consider, among other things, the dilutive impact, if any, on our stockholders, the ability to leverage stockholder returns through debt financing, the particular terms and conditions of each alternative financing arrangement and our ability to service our obligations under such financing arrangements.

As of ~~June~~March 3031, ~~2006~~2009, we had cash, cash equivalents and marketable securities of ~~approximately~~ ~~$26.8 million.~~approximately ~~Of this amount,~~ $53.5 million ~~is currently held in a restricted account to serve as collateral for our long-term debt~~. ~~Our funds are currently invested in investment grade and United~~ ~~States government securities.~~

Clinical Data Secured Loan

As a part of the proposed merger, we entered into a note purchase agreement with Clinical Data pursuant to which Clinical Data made a series of loans to us evidenced by term notes in the aggregate principal amount of $4 million. The term notes bear interest at a fixed rate of 7% per annum and mature on May 31, 2009 unless accelerated pursuant to their terms. The original amount of the loan from Clinical Data under the note purchase agreement was $3 million and matured on March 31, 2009. On January 12, 2009, Clinical Data extended the maturity of the original $3 million term note evidencing the loan until April 30, 2009. On March 30, 2009, Avalon and Clinical Data amended the note purchase agreement and the original $3 million term note to further extend the $3 million term note’s maturity date to May 31, 2009 and Clinical Data and Avalon also increased the amount borrowed by Avalon under the note purchase agreement from $3 million to $4 million through the issuance by Avalon of an additional $1 million term note. We have the right to prepay the term notes, together with any accrued interest, at any time without penalty. The maturity of the term notes accelerates if there is a default under the terms of the note purchase agreement or related documents, including any default, breach or termination of Clinical Data’s license agreement with us relating to AvalonRx® or of the merger agreement (other than a termination of the merger agreement as a result of a failure to obtain the approval by our stockholders of the merger). The term notes are secured by collateral consisting of certain of our intellectual property rights.

Sources and Uses of Cash

Operating Activities. Net cash used in operating activities for the ~~six~~three months ended ~~June~~ March 3031, ~~2006~~ 2009 was $63.13 million, compared to $64.98 million for the same period in fiscal ~~2005~~2008. During the first ~~six~~three months of fiscal year ~~2006~~2009, our net loss of $93.06 million was reduced by non-cash charges of $~~2.9 million~~430,000, primarily ~~associated~~for ~~with the issuance of~~ stock ~~options~~compensation, depreciation and amortization, offset ~~and~~by ~~reduction~~changes in our net operating assets and liabilities. ~~Net operating assets and~~ liabilities declined due to a $731,000 decrease in accounts payable and accrued liabilities, of which $718,000 was directly related to payment of 2005 year end performance bonuses. This decrease was offset, in part, by a $598,000 increase in accounts receivable and other assets.

Investing Activities. Net cash ~~used~~provided inby investing activities for the ~~six~~three months ended ~~June~~March 3031, ~~2006~~ 2009 was $~~4.5 million~~894,000, compared to net cash used in investing activities of $54.1 2 million for the same period in 2008. Proceeds from the sale and maturity of ~~cash~~marketable ~~provided~~securities were bythe primary source of cash from investing activities, ~~during~~providing $899,000 in the first three ~~same~~months ~~period~~of 2009 and $9.2 million in ~~2005~~the comparable period of 2008. Cash used in investing activities principally represents the amount used to purchase marketable securities, net of proceeds from the sale and maturity of marketable securities.

Financing Activities. Net cash provided by financing activities for the ~~six~~three months ended ~~June 30~~March 31, ~~2006~~2009 was $51.20 million, compared to $~~2.9 million~~43,000 of net cash used in financing activities for the same period in ~~2005~~2008. ~~During~~In ~~the~~March 2009, ~~first six~~we ~~months~~borrowed ofan ~~2006,~~additional $71.30 million ~~was raised~~ from ~~issuance~~Clinical Data ofunder ~~common~~a ~~stock.~~secured ~~This~~loan ~~amount~~to ~~was~~fund ~~offset by~~our ~~$1.8 million~~short-term ~~repayments on debt~~operations.

Page 11

Credit Arrangements

In April 2003, we entered into a series of agreements with the Maryland Industrial Development Financing Authority, or MIDFA, and Manufacturers and Traders Trust Company, or M&T Bank, in order to finance improvements to our corporate office and research facility located in Germantown, Maryland. MIDFA sold development bonds in the amount of $12.0 million. The proceeds of the bond sale were put in trust to reimburse us for the costs we incurred for improvements to our facility. We are required to repay the trust $1.2 million annually for these borrowings. The borrowing bears interest at a variable rate and matures on April 8, 2013. The weighted-average interest rate during the six months ended June 30, 2006 and 2005 was 4.92% and 2.99% respectively.

In connection with the development bond financing, we entered into an agreement with M&T Bank to issue the trustee an irrevocable letter of credit to provide payment of the principal and interest of the bonds. The amount of the letter of credit changes annually, as principal payments are made. As of June 30, 2006, that amount is $8,538,082, consisting of $8.4 million of principal and $138,082 in interest, computed at 50 days at an assumed maximum rate of interest of 12% per annum. The letter of credit expires the earlier of April 8, 2008, or the date the bonds have been paid in full. In consideration of the letter of credit, we have granted M&T Bank a security interest in certain facility improvements, equipment and cash collateral held as restricted cash. In August 2005 we entered into a modification agreement with M&T Bank and MIDFA pursuant to which M&T Bank agreed to waive our compliance with the financial covenants contained in the letter of credit until April 2006 in exchange for increasing the amount of cash collateral held as restricted cash to $6.3 million. On April 1, 2006 the waiver expired and the cash collateral amount held as restricted cash was reduced to $5.5 million. The Company is in compliance with all financial covenants contained in the Company’s letter of credit.

In June 2002, we entered into an equipment line of credit with General Electric Capital Corporation that provided for borrowings of up to $5.0 million. In 2003, the line of credit was increased to allow for an additional $2.0 million in borrowings. During 2002 and 2003 a total of $5.6 million was borrowed by us under the equipment line of credit. No draws were made during 2004 and the availability of the line of credit has lapsed. Each draw has been treated as a separate promissory note bearing interest between 7.09% to 8.68% over 36- to 48-month terms. The line of credit is secured by the applicable equipment, fixtures, and personal property financed by the line of credit. In connection with draws under the line of credit, the lender received warrants to purchase a total of 39,306 shares of our Series B preferred stock at an exercise price of $3.53, which subsequently automatically converted into warrants to purchase 8,666 shares of common stock at an exercise price of $28.24 per share in connection with the closing of our initial public offering. At June 30, 2006, roughly $760,000 in borrowings remained outstanding under this line of credit.

Operating Capital and Capital Expenditure Requirements

We expect to continue to incur substantial operating losses in the future. We will not receive any product revenue until a drug candidate has been approved by the FDA or similar regulatory agencies in other countries and successfully commercialized. We currently anticipate that our cash, cash equivalents and marketable securities, together with cash flow generated from our collaborations, will be sufficient to fund our operations at least through the next eighteen months. However, we will need to raise substantial additional funds to continue our operations and bring future products to market. We cannot be certain that any of our programs will be successful or that we will be able to raise sufficient funds to complete the development and commercialization of any of our drug candidates currently in development, should they succeed. Additionally, we plan to continue to evaluate in-licensing and acquisition opportunities to gain access to new drugs or drug targets that would fit with our strategy. Any such transaction would likely increase our funding needs in the future.

Our future funding requirements will depend on many factors, including but not limited to:

• the size and complexity of our research and development programs; • the scope and results of our preclinical testing and clinical trials; • continued scientific progress in our research and development programs; • the time and expense involved in seeking regulatory approvals; • competing technological and market developments; • acquisition, licensing and protection of intellectual property rights; and • the cost of establishing manufacturing capabilities and conducting commercialization activities.

Until we can generate a sufficient amount of product revenue to finance our cash requirements, which we may never do, we expect to finance future cash needs primarily through public or private equity offerings, debt financings or strategic collaborations. If we are successful in raising additional funds through the issuance of equity securities, investors likely will experience dilution, or the equity securities may have rights, preferences or privileges senior to those of the holders of our common stock. If we raise funds through the issuance of debt securities, those securities would have rights, preferences and privileges senior to those of our common stock. We do not know whether additional funding will be available on acceptable terms, or at all. If we are not able to secure additional funding when needed, we may have to delay, reduce the scope of, or eliminate one or more of our clinical trials or research and development programs. In addition, we may have to partner one or more of our drug candidate programs at an earlier stage of development, which would lower the economic value of those programs to our company.

Page 12

Item 3. Quantitative and Qualitative Disclosures About Market Risk

~~We are exposed to market risk from changes in interest rates. At June 30, 2006, we had $8.4~~ ~~million~~Not ofapplicable ~~obligations~~pursuant ~~which were subject~~ to ~~variable~~the ~~rates~~rules of ~~interest under our development bond financing with MIDFA. If market interest rates increased 1% from~~ the ~~rate~~Securities atand ~~June 30,~~Exchange ~~2006,~~Commission ~~our~~relating ~~annual~~to ~~interest~~the ~~expense~~disclosure ~~would~~requirements ~~increase~~for ~~approximately~~a ~~$84,000,~~“smaller ~~assuming~~reporting ~~that obligations subject to variable interest rates remained constant~~company.”

InItem 4T. ~~addition,~~Controls ~~the value of our portfolio of cash equivalents~~ and ~~investments is subject to~~Procedures ~~market risk from changes in interest rates.~~

~~The primary objective of our investment activities is to preserve our capital for the purpose~~ ofDisclosure ~~funding~~Controls ~~operations~~and ~~while~~Procedures: atUnder the ~~same~~supervision ~~time~~and ~~maximizing~~with the ~~income~~participation weof our ~~receive~~management, ~~from~~including our ~~investments without~~Chief ~~significantly~~Executive ~~increasing~~Officer ~~risk.~~and Toour ~~achieve~~Chief ~~these~~Financial ~~objectives~~Officer, ~~our~~we ~~investment policy allows us~~have toevaluated ~~maintain~~the aeffectiveness ~~portfolio~~ of ~~cash~~our ~~equivalents~~disclosure controls and ~~investments~~procedures, inas ~~a variety~~ of ~~securities~~March 31, ~~including~~2009 (the ~~commercial~~“Evaluation ~~paper,~~Date”). ~~money~~Based ~~market~~on ~~funds~~that ~~and~~evaluation, ~~corporate~~our ~~debt~~Chief ~~securities.~~Executive AsOfficer ofand ~~June 30,~~Chief ~~2006, we had~~Financial ~~cash~~Officer ~~and~~have ~~cash~~concluded ~~equivalents~~that, ~~short-term~~as ~~and~~of ~~long-term~~the ~~investments~~Evaluation ~~and~~Date, ~~restricted~~our ~~cash~~disclosure ofcontrols ~~$26.8 million~~and asprocedures ~~follows:~~were effective.

Cash and cash equivalents		$4.4 million
Short-term investments		$16.1 million
Long-term investments		$0.8 million
Restricted cash		$5.5 million

We maintain an investment portfolio of investment grade government agency notes and corporate bonds. The securities in our investment portfolio are not leveraged, are classified as available-for-sale and are, due to their predominantly short-term nature, subject to minimal interest rate risk. We currently do not hedge interest rate exposure on our investment portfolio. As of June 30, 2006, securities totaling $16.1 million mature in the next 12 months and $.8 million mature after June 30, 2007. While we do not believe that an increase in market rates of interest would have any significant negative impact on the realizable value of our investment portfolio, changes in interest rates affect the investment income we earn on our investments and, therefore, impact our cash flow and results of operations.

We have operated in the United States and all revenues to date have been received in U.S. dollars. Accordingly, we have not had any material exposure to foreign currency rate fluctuations.

Item 4. Controls and Procedures

Disclosure Controls and Procedures: Under the supervision and with the participation of our management, including our Chief Executive Officer and our Chief Financial Officer, we have evaluated the effectiveness of our disclosure controls and procedures, as of June 30, 2006 (the “Evaluation Date”). Based on that evaluation, our Chief Executive Officer and Chief Financial Officer have concluded that, as of the Evaluation Date, our disclosure controls and procedures were effective.

Changes in Internal Control over Financial Reporting: There have been no changes in our internal control over financial reporting during the quarter ended on the Evaluation Date that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

~~Page~~ 13

PART II. OTHER INFORMATION

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

(a) and (c)

Not applicable

(b) Use of Proceeds

On September 28, 2005, our Registration Statement on Form S-1 (333-124565) covering our initial public offering was declared effective by the Securities and Exchange Commission. From the effective date of our Registration Statement on Form S-1 through June 30, 2006, we have utilized approximately $11.5 million of the net proceeds of our initial public offering to fund our operations and approximately $2.5 million to make interest and principal payments under our loan agreement with MIDFA and equipment financing arrangement with GE Capital.

Item 4. Submission of Matters to a Vote of Security Holders

Our stockholders voted on three items at the Annual Meeting of Stockholders held on June 9, 2006:

1. The election of nine directors to serve on our Board of Directors for a term of one year and until their successors are elected and qualified: 2. The amendment of our 2005 Omnibus Long-Term Incentive Plan (the “Incentive Plan”) to increase the number of shares available for issuance under the Incentive Plan from 989,738 shares to 1,581,582 shares; and 3. Ratification of the appointment of Ernst & Young LLP as our independent public accounting firm for the fiscal year ending December 31, 2006.

The nominees for director were elected based on the following votes:

Nominee	Votes For		Votes Withheld
Alan G. Walton, Ph.D., D.Sc.		7,215,157		17,900
Kenneth C. Carter, Ph.D.		6,756,657		476,400
Michael R. Kurman, M.D.		7,019,320		213,737
Bradley G. Lorimier		7,216,657		16,400
Ivor Royston, M.D.		7,216,157		16,900
William A. Scott, Ph.D.		7,215,157		17,900
Patrick Van Beneden		6,934,220		298,837
William H. Washecha		7,216,657		16,400
Raymond J. Whitaker, Ph.D.		7,216,157		16,900

The proposal to amend the Incentive Plan to increase the number of shares available for issuance under the Incentive Plan from 989,738 shares to 1,581,582 shares received the following votes:

• 5,128,275 votes for approval • 39,164 votes against • 879,490 abstentions

There were 181,005 broker non-votes for this item.

The proposal to ratify the appointment of Ernst & Young LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2006 received the following votes:

• 7,219,196 votes for approval • 6,511 votes against • 7,350 abstentions

There were 1,367,163 broker non-votes for this item.

Page 14

Item 6. Exhibits

Exhibit No.		Description
Exhibit
10.1		Avalon Pharmaceuticals, Inc. 2005 Omnibus Long-Term Incentive Plan, as amended (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K filed on June 13, 2006)
No.		Description
31.1		Certification of Chief Executive Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 (filed herewith)
2.1(1)		First Amendment to Agreement and Plan of Merger and Reorganization, dated as of January 12, 2009, by and among Clinical Data, Inc., API Acquisition Sub II, LLC and Avalon Pharmaceuticals, Inc.
31.2		Certification of Chief Financial Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 (filed herewith)
2.2(2)		Second Amendment to Agreement and Plan of Merger and Reorganization, dated as of March 30, 2009, by and among Clinical Data, Inc., API Acquisition Sub II, LLC and Avalon Pharmaceuticals, Inc. (included as Annex A to the proxy statement/prospectus).
32.1		Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350 as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (filed herewith)
10.1(2)		First Amendment to Note Purchase Agreement, dated March 30, 2009, between Clinical Data, Inc. and Avalon Pharmaceuticals, Inc. (included as Annex I to proxy statement/prospectus).
10.2(1)		Amendment No. 1 to Term Note, dated January 12, 2009.
10.3(2)		Amendment No. 2 to Term Note, dated March 30, 2009.
10.4(2)		Term Note, dated March 30, 2009, issued by Avalon Pharmaceuticals, Inc. to Clinical Data, Inc.
31.1		Certification of Chief Executive Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2		Certification of Chief Financial Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1		Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350 as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

Page 15


(1)		Incorporated by reference to our Current Report on Form 8-K filed on January 14, 2009.

(2)		Incorporated by reference to our Current Report on Form 8-K filed on April 2, 2009.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

	AVALON PHARMACEUTICALS, INC.
Date: August 14, 2006	By:	/s/ Kenneth C. Carter
Date: May 13, 2009	By:	/s/ Kenneth C. Carter
		Kenneth C. Carter, Ph.D.
		President, Chief Executive Officer and Director (Principal Executive Officer)
Date: May 13, 2009	By:	/s/ C. Eric Winzer
		C. Eric Winzer
		Executive Vice President and Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer)

Date: August 14, 2006	By:	/s/ Gary Lessing
		Gary Lessing
		Executive Vice President and Chief Financial Officer (Principal Financial Officer)

Date: August 14, 2006	By:	/s/ Glen Farmer
		Glen Farmer
		Controller (Principal Accounting Officer)

Page 16

Filing Compare · AVALON PHARMACEUTICALS INC