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UNITED STATES SECURITIES AND
    EXCHANGE COMMISSION
 Washington, D.C.
    20549
  Form 10-K
  þ

ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d)  OF THE
    SECURITIES EXCHANGE ACT OF 1934For the fiscal year ended
    March 31, 2009ORo

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)  OF
    THE SECURITIES EXCHANGE ACT OF 1934For the transition period
    from          to   Commission File
    No. 0-12716
  CLINICAL DATA, INC.
 (Exact Name of Registrant as
    Specified in its Charter)
  Delaware

04-2573920(State or Other Jurisdiction
    of
    Incorporation or Organization)

(I.R.S. Employer
    Identification No.)One Gateway Center, Suite 702,
    Newton, Massachusetts(Address of Principal
    Executive Offices)

02458(Zip
    Code)   Registrants telephone number, including area code:
 (617) 527-9933
  Securities registered pursuant to Section 12(b) of the
    Act:
  Common Stock, $.01 par value

The NASDAQ Stock Market LLC
    (NASDAQ Global Market)   Securities registered pursuant to Section 12(g) of the
    Act:
  o þ
  o þ
  þ o
  Regulation S-T o o
  Regulation S-K Form 10-K Form 10-K. þ
  12b-2
  Large
    accelerated
    filer o
    Accelerated
    filer þ
    Non-accelerated
    filer o
    Smaller
    reporting
    company o   Rule 12b-2 o þ
      DOCUMENTS
    INCORPORATED BY REFERENCE




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##### 





INDEX TO
    FORM 10-K
  FOR THE
    FISCAL YEAR ENDED MARCH 31, 2009
   
 PagePART 1ITEM 1.


Business


1ITEM 1A.


Risk Factors


16ITEM 1B.


Unresolved Staff Comments


30ITEM 2.


Properties


31ITEM 3.


Legal Proceedings


31ITEM 4.


Submission of Matters to a Vote of Security
    Holders


31PART IIITEM 5.


Market for Registrants Common Equity,
    Related Stockholder Matters and Issuer Purchases of Equity
    Securities


31ITEM 6.


Selected Consolidated Financial Data


33ITEM 7.


Managements Discussion and Analysis of
    Financial Condition and Results of Operations


35ITEM 7A.


Quantitative and Qualitative Disclosures about
    Market Risk


44ITEM 8.


Financial Statements and Supplementary Data


45ITEM 9.


Changes in and Disagreements with Accountants on
    Accounting and Financial Disclosure


45ITEM 9A.


Controls and Procedures


45ITEM 9B.


Other Information


48PART IIIITEM 10.


Directors, Executive Officers and Corporate
    Governance


48ITEM 11.


Executive Compensation


48ITEM 12.


Security Ownership of Certain Beneficial Owners
    and Management and Related Stockholder Matters


48ITEM 13.


Certain Relationships and Related Transactions
    and Directors Independence


48ITEM 14.


Principal Accounting Fees and Services


48PART IVITEM 15.


Exhibits, Financial Statement Schedules


48SIGNATURES


49EX-4.2 Specimen Certificate of Contingent Value Rights to receive common stockEX-21.1 Subsidiaries of the CompanyEX-23.1 Consent of Deloitte & Touche LLPEX-31.1 Certification of Chief Executive Officer Pursuant to Section 302EX-31.2 Certification of Chief Financial Officer Pursuant to Section 302EX-32.1 Certification of Chief Executive Officer and Chief Financial Officer pursuant to Section 906    ® tm FAMILION ®




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NOTE REGARDING
    FORWARD-LOOKING STATEMENTS
  Form 10-K Form 10-K. Form 10-K Form 10-K.
  WHERE YOU
    CAN FIND MORE INFORMATION
  1-800-SEC-0330 http://www.sec.gov http://www.clda.com.




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PART I  ITEM 1.
    BUSINESS  General
    first-in-class best-in-category
  Vilazodone
  1A in vitro In
    vitro 1A 1A 5-HT 1A Journal of Clinical
    Psychopharmacology 19(3):
    268-71,
    1999
        Stedivaze
  2A best-in-category
 1




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best-in-category
  Other
    Therapeutic Compounds
  2A 2B
  FAMILION
  Company
    History
    FAMILION
    FAMILION
   2




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2A best-in-category
      first-in-class, best-in-category
    OUR
    INDUSTRIES
  Therapeutic
    Development
  in vitro in vivo and/or
   3




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Targeted
    Therapeutics
  trial-and-error Institute of Medicine of the National
    Academies, 2006
      
    the ability to identify and develop through toxicology, PK and
    PD pre-clinical studies to
    first-in-human
    trials;
    the ability to integrate our technologies into the overall
    development program;
    the ability to establish efficacy and safety in a clinical
    development program;
    the ability to gain marketing approval from the FDA and other
    regulatory agencies;
    the ability to identify early in the drug development process
    biomarkers that will enable the clinical development program
    with the potential for clinical utility;
    the complexity of the disease or syndrome being addressed;
    the complexity of the determinants of drug response which may
    include host genetic, tumor genetics, environment, culture, age,
    and other interactions;
    reimbursement policies;
    the ability of patents to protect both the drug and the
    diagnostic; and
    the ability of the drug to compete in the marketplace against
    current and future products. 4




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Genetic
    Biomarker Test Development and Commercialization
  SG Cowen  2001
  FAMILION
    
    the ability to patent protect genetic biomarkers and its
    clinical utility;
    operating within an antiquated reimbursement system that does
    not reflect either the investment to develop or the clinical or
    economic value of the test;
    demonstrating data to support test adoption and reimbursement;
    educating providers on the value of incorporating genetic
    testing into their practice;
    the potential for unduly burdensome regulation of these tests;
    establishing validated genetic tests with adequate predictive
    characteristics;
    the complexity of the genetic underpinnings of disease, and the
    related complexity of identifying and validating genetic
    biomarkers;
    other parties who have opposing interests in the
    commercialization of these tests as they threaten their business
    models or markets; and
    ethical, legal, regulatory, and social considerations.   5




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OUR
    COMPANY
  Our
    Strategy
  first-in-class and/or best-in-category and/or
  Our
    Pharmaceutical Pipeline
  Vilazodone
  About
    Depression
  Rush, et al.
    Am J Psychiatry. November 2006 ;163(11):1905-17 sub-optimally 5-HT 1A
    sub-optimally 5-HT 1A
  Market
    Opportunity and Competition
   6




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first-in-class 5-HT 1A
  About
    Vilazodone
  1A in vitro In vitro 1A 1A Journal of Medicinal Chemistry 47:
    4684-4692,
    2004 5-HT 1A 1A
  Journal of
    Clinical Psychiatry
     7




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Stedivaze
  Overview
  2A best-in-category
  About
    Myocardial Perfusion Imaging
  and/or
  Market
    Opportunity and Competition
  2A 1 2B 3
 8




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1 2B 2A
  About
    Stedivaze
  2A 2A 2A 2A
  Pre-clinical
    Programs
  ATL844
  and/or Malthon,
    Daniel (18 June 2007). Asthma & COPD 
    Clearing the air World
    Diabetes Market Analysis,
    2009-2023,
    ReportLinker.com 2B sub-type.
  ATL1222
  2A
  ATL313
  2A
 9




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AVN316
      Strategic
    Acquisitions
  pre-clinical
  Our
    Genetic Tests
  Developing
    and Commercializing Genetic Tests
  FAMILION FAMILION
  FAMILION
  Sales and
    Marketing
  FAMILION
 10




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The
    FAMILION Family of Tests
  Sudden Arrhythmia
    Death Syndromes Foundation (SADS) citing CDC 2002
    
    aids in the diagnosis of disease;
    aids in comprehensive risk assessment;
    guides lifestyle modifications;
    provides information needed to develop a comprehensive treatment
    plan, which may include the placement of an internal
    cardioverter defibrillator;
    determines if family members are at risk, including those who
    are currently asymptomatic; and
    provides important information for genetic counseling.  FAMILION FAMILION FAMILION
  SADS Foundation Priori SG, et al.,
    Circulation 1999;99:529-33
  QT-interval Priori SG, et al., Circulation 1999;
    99:529-33 FAMILION
  30-50% Mohamed U, et al. J Cardiovasc Electrophysiol. 2007;
    18(7):791-7 Priori SG, et al., Circulation, 2002;106:69-74
  Keren A, et al., Nature.2008; 5(3):158-68
 11




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Prasad et al., Heart. 1999;
    82:8-15
  Keren, et al, Nature 2008; 5(3);
    158-68 Prasad, et al., Heart
    1999; 82:8-15
  Muthappan P, Calkins H. Prog Cardiovasc Dis. 2008;51:31-43,
    Peters S. Int J Cardiol. 2006;113:4-11
  McKenna WJ et al. Br Heart J. 1994;71(3):215-218]. Sen-Chowdry
    S, et al. J Am Coll Cardiol. 2007;50:1813-1821
  Volume 15, Issue 2, Pages
    83-97 . s
  ACC/AHA/ESC 2006 Guidelines for Management
    of Patients With Ventricular Arrhythmias and the Prevention of
    Sudden Cardiac Death Circulation [2006;114;1088-1132
  FAMILION
 12




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out-of-pocket
  Challenges
    in Reimbursement
  case-by-case
  FAMILION
  FAMILION FAMILION FAMILION FAMILION in-network FAMILION FAMILION
  OTHER
    BUSINESS MATTERS
  Government
    Regulation
       13




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FAMILION
  In Vitro
      Patents
    and Proprietary Technology
     14




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2A 2B
    
    Ten issued United States patents, two pending United States
    patent applications, two-hundred eight-three issued foreign
    patents, and ninety-eight pending foreign patent applications
    owned by Merck relating to vilazodone, methods for manufacturing
    vilazodone, and methods of using vilazodone to treat depression
    and other anxiety disorders;
    Four issued United States patents, one pending United States
    patent application, two pending United States provisional patent
    applications, sixty-eight issued foreign patents, and fifteen
    pending foreign patent applications owned by the University of
    Virginia Patent Foundation relating to Stedivaze compositions
    and methods of using Stedivaze for myocardial perfusion imaging
    and other imaging modalities;
    One issued United States patent owned by the University of
    Massachusetts relating to a use for Stedivaze;
    One issued United States patent co-owned by the University of
    Virginia Patent Foundation and Penn State Research Foundation
    relating to methods for improving insulin sensitivity or
    stimulating glucose uptake;
    One pending United States patent application, and four pending
    foreign patent applications owned by the National Institutes of
    Health relating to methods for treating cancer;
    Ten issued United States patents, twelve pending United States
    patent applications, one pending United States provisional
    patent application, seven issued foreign patents, seventeen
    pending foreign patent applications, and one pending
    international patent application under the Patent Cooperation
    Treaty owned by the University of Virginia Patent Foundation
    relating to our substantial adenosine-related product pipeline;
    One co-owned pending international patent application under the
    Patent Cooperation Treaty relating to an ophthalmic indication;
    Five issued United States patents, three issued foreign patents,
    and seven pending foreign patent applications owned by the
    University of Utah relating to the diagnosis of inherited LQTS;
    Five issued United States patents, six issued foreign patents,
    and three pending foreign patent applications owned by Genzyme
    Corporation relating to the diagnosis of inherited LQTS;
    One pending United States patent application, two pending
    foreign patent applications, and one pending international
    patent application under the Patent Cooperation Treaty relating
    to the diagnosis of inherited ARVC;
    Three pending United States patent applications, three issued
    foreign patents, and five pending foreign patent applications
    owned by CHU Tours relating to the use of the FCGR3A V158F
    variant to predict certain phenotypes, including rituximab
    efficacy;
    One issued United States patent controlled by Innate Pharma
    relating to genotyping the FCGR3A V158F variant;
    One pending United States patent application owned by the
    University of Alabama-Birmingham relating to the use of certain
    FCGR2B variants to predict certain phenotypes;
    One issued United States patent owned by St. Jude
    Childrens Research Hospital (exclusively sublicensed to
    Prometheus Laboratories Inc. and Specialty Laboratories, Inc.)
    relating to genetic markers predictive of thiopurine toxicity;
    One issued United States patent owned by Yale University
    (exclusively sublicensed to Siemens Medical Solutions
    Diagnostics) relating to the coupled amplification and
    sequencing of DNA; and
    One issued United States patent owned by Vanderbilt University
    relating to a genetic marker predictive of drug-induced cardiac
    arrhythmia. 15




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Backlog
    Employees
    Environmental
    Matters
    Significant
    Customers
    Discontinued
    Operations
    Investor
    Information
  http://www.clda.com Form 10-K, Form 10-Q, Form 8-K,
  ITEM 1A.
    RISK
    FACTORS    Risk
    Factors Relating to Our Business and Operations
  Without
    additional capital raising opportunities, or a significant
    change in our operating and development plan, we will not have
    sufficient cash resources available to fund our current level of
    activities beyond December 2009, including our New Drug
    Application submission for vilazodone and Phase III
    clinical trial programs for Stedivaze.
   16




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
    partnering opportunities with pharmaceutical or biotechnology
    companies for development and marketing of our late-stage or
    pre-clinical compounds;
    sale of non-core assets; and/or
    sale of equity or debt securities.      Given
    our current product development efforts which have resulted in
    significant net losses, we expect to incur net losses for the
    foreseeable future.
      If
    regulatory authorities fail to timely approve vilazodone for
    marketing, our results of operations will suffer.
     17




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Personalized
    medicine and pharmacogenomics is an emerging field, and
    therefore regulatory approval of our drug candidates that are
    paired with a companion diagnostic and diagnostic tests may take
    longer and be less predictable than approval for untargeted
    medicines.
  and/or
    If our
    assumption about the role of genes in diseases or drug response
    is wrong, we may not be able to develop useful
    products.
    We may
    not successfully develop or derive revenues from any
    products.
  and/or
  
    establish that they are safe and effective;
    establish that they are clinically valid and useful;
    successfully compete with other technologies and products;
    ensure that they do not infringe on the proprietary rights of
    others;
    establish that they can be manufactured in sufficient quantities
    at reasonable costs;
    obtain and maintain regulatory approvals for them; and
    market them successfully. 18




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We may
    not derive significant revenues from our diagnostic
    tests.
  FAMILION
  If
    physicians and patients do not accept and use our tests and
    drugs, we will not achieve sufficient product revenues and our
    business will suffer.
    
    perceptions by members of the healthcare community, including
    physicians, about the safety and effectiveness of our drugs;
    published studies demonstrating the cost-effectiveness of our
    drugs relative to competing products;
    accuracy and reliability of our laboratory testing;
    availability of reimbursement for our products from government
    or healthcare payers; and
    effectiveness of marketing and distribution efforts by us and
    our licensees and distributors, if any.    If our
    products are not granted adequate reimbursement from third-party
    payers, we may be unable to successfully commercialize our
    products and we may never achieve widespread market acceptance
    of our products.
      We
    recently have entered into new business areas and may not have
    the expertise, experience and resources to pursue all of our
    businesses at once.
   19




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If we
    are unable to develop and/or in-license or otherwise acquire new
    products and technologies, we may not be able to grow our
    company successfully.
  and/or
  Due to
    our recent acquisitions and dispositions, it may be more
    difficult to obtain additional financing at favorable terms, if
    at all.
    Because
    a significant portion of our total assets are represented by
    goodwill that is subject to mandatory annual impairment
    evaluations, we could be required to write-off some or all of
    this goodwill which may adversely affect our financial condition
    and results of operations.
    We may
    be unable to successfully complete the integration of the
    businesses of Adenosine Therapeutics and Avalon.
    
    retaining existing customers and strategic partners of each
    company; 20




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
    coordinating research and development activities to enhance
    introduction of new products and technologies, especially in
    light of rapidly evolving markets for those products and
    technologies;
    preserving the value of various research and development,
    collaboration, distribution, manufacturing and other important
    relationships;
    effectively managing the diversion of management attention from
    business matters to integration issues;
    eliminating corporate overhead and consolidating administrative
    functions;
    combining product offerings and incorporating acquired
    technology and rights into product offerings effectively and
    quickly; and
    developing and maintaining uniform standards, controls,
    procedures and policies.  We may
    not be able to successfully integrate companies that we acquire
    in the future.
      
    difficulties in integrating the operations, technologies and
    products of the acquired companies;
    the risk of diverting managements attention from normal
    daily operations of the business;
    potential difficulties in completing projects associated with
    in-process research and development;
    risks of entering markets in which we have no or limited direct
    prior experience and where competitors in such markets have
    stronger market positions;
    initial dependence on unfamiliar supply chains or relatively
    small supply partners;
    insufficient revenues to offset increased expenses associated
    with the acquisition; and
    the potential loss of key employees of the acquired companies.    We are
    dependent upon certain key personnel.
    In
    order to conduct clinical trials and to market our drugs, we
    will have to develop methods to produce these drugs using
    approved methods and at commercially viable rates.
   21




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If we
    cannot successfully form and maintain suitable arrangements with
    third parties for the manufacturing of the products we may
    develop, our ability to develop or deliver products may be
    impaired.
      New
    drug and genetic and pharmacogenetic test development involves a
    lengthy and complex process, and we may be unable to
    commercialize any of the products we develop.
      
    collect and analyze DNA samples;
    conduct association studies to discover and replicate
    relationships between genetic variations in the DNA samples and
    phenotype of interest;
    undertake clinical trials to validate the efficacy, safety,
    toxicology, pharmacology, pharmacokinetics and other aspects of
    our drug candidates, and predictiveness of any related
    diagnostic tests;
    expend significant resources;
    maintain and expand our intellectual property rights;
    obtain, where necessary, marketing approvals from the FDA and
    other regulatory agencies; and
    find collaborative partners with manufacturing and commercial
    capabilities for our current and future drug candidates and
    related diagnostics.    
    the failure of products in the research and development stage;
    the high cost of clinical trials and our lack of financial and
    other resources;
    the inability to locate partners with sufficient resources to
    assist in conducting clinical trials; and
    the lack of clinical validation data to support the validity and
    utility of our products.   22




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Our
    operations may be affected by unexpected problems frequently
    encountered in connection with the development and transition to
    other technologies and by the competitive environment in which
    we operate.
    The
    covenants in the convertible notes restrict our financial and
    operational flexibility.
    Risk
    Factors Relating to Our Intellectual Property
  If we
    are unable to protect effectively our intellectual property, we
    may not be able to operate our business and third parties may
    use our technology, both of which would impair our ability to
    compete in our markets.
      
    pending patent applications may not result in issued patents;
    the claims of any issued patents may not provide meaningful
    protection;
    the claims of any issued patents may be invalidated or held
    unenforceable under current law or upon changes in patent law:
    we may be unsuccessful in developing additional proprietary
    technologies that are patentable; 23




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
    our patents may not provide a basis for commercially viable
    products or provide us with any competitive advantages and may
    be challenged by third parties; and
    others may have patents that relate to our technology or
    business.      If
    third parties make or file claims of intellectual property
    infringement against us, or otherwise seek to establish their
    intellectual property rights, we may have to spend time and
    money in response and cease some of our
    operations.
    Any
    patent protection we obtain for our products may not prevent
    marketing of similar competing products.
      Any
    patents we obtain may be challenged by producers of generic
    drugs.
   24




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Patents
    pending may not issue.
    We may
    be unable to achieve milestones contained in our licensing
    agreements and have our license revoked by our
    licensors.
    Risk
    Factors Relating to Regulatory Matters
  Pre-clinical
    and clinical trials are time consuming, expensive, and uncertain
    processes.
  pre-clinical pre-clinical Pre-clinical
    
    the size of the patient population;
    the proximity of patients to clinical sites;
    the eligibility criteria for the trial;
    alternative therapies or technologies; and
    competing clinical trials and new drugs approved for the
    conditions or indications we are investigating.     25




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
    we must demonstrate through clinical trials that the proposed
    product is safe and effective for its intended use;
    we have limited experience in conducting the clinical trials
    necessary to obtain regulatory approval; and
    data obtained from pre-clinical and clinical activities are
    susceptible to varying interpretations which could delay, limit
    or prevent regulatory approvals.    and/or
  Even
    if our drug candidates obtain regulatory approval, we will be
    subject to on-going government regulation.
       26




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We
    have only limited experience in regulatory affairs which may
    affect our ability or the time we require to obtain necessary
    regulatory approvals.
    Third
    parties engaged to produce our drug candidates for clinical use
    may fail to comply with regulatory requirements, which could
    harm our clinical trials.
    Our
    operations involve hazardous materials and medical waste and are
    subject to environmental, health and safety controls and
    regulations Any claim relating to our improper handling, storage
    or disposal of biological and hazardous materials could be
    time-consuming and costly, and may exceed our
    resources.
      Our
    business involves animal testing and changes in laws,
    regulations or accepted clinical procedures or social pressures
    could restrict our use of animals in testing and adversely
    affect our research and development efforts.
      Risk
    Factors Relating to Our Industry
  Concerns
    regarding the use of genetic testing results may limit the
    commercial viability of any products we develop.
   27




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and/or
  If we
    were sued for product liability, we could face substantial
    liabilities that may exceed our resources.
    We may
    not be able to compete successfully with other companies and
    government agencies in the development and marketing of products
    and services.
          
    develop proprietary products;
    develop and maintain products that reach the market first, and
    are technologically superior to and more cost effective than,
    other products on the market;
    obtain patent or other proprietary protection for our products
    and technologies;
    attract and retain scientific and product development personnel;
    obtain required regulatory approvals; and
    manufacture, market and sell products that we develop. 28




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Intense
    competition could reduce our market share or limit our ability
    to increase market share, which could harm our financial
    performance.
    
    develop technologies, products and services that are more
    effective than our products or services, or that render our
    technologies, products or services obsolete or noncompetitive;
    obtain patent protection or other intellectual property rights
    that would prevent us from developing our potential
    products; or
    obtain regulatory approval for the commercialization of their
    products more rapidly or effectively than we do.    We
    operate in a very competitive environment.
    
    diagnostic and pharmaceutical companies;
    companies developing drug discovery technologies;
    companies developing molecular diagnostic and genetic
    tests; and
    companies developing point-of-care diagnostic and genetic tests.      Risk
    Factors Relating to Our Common Stock
  Future
    sales of our common stock or other securities may dilute our
    stockholders.
   29




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If the
    investors in our private placements sell their shares, which
    have been registered under the Securities Act, the market price
    of our common stock may decline significantly.
    Our
    ownership is concentrated among a small number of
    stockholders.
    The
    price of our common stock is volatile and could cause investors
    to lose a substantial part of their investment.
    
    the timing of our announcements or of our competitors
    announcements regarding significant products, contracts or
    acquisitions;
    variations in results of operations;
    changes in earnings estimates by securities analysts;
    general economic and market conditions; and
    sales of substantial amounts of our common stock into the public
    market, or the perception that such sales might occur.  We may
    issue preferred stock with rights that could affect your rights
    and prevent a takeover of the business.
    We
    currently do not intend to pay dividends on our common stock and
    consequently, your only opportunity to achieve a return on your
    investment is if the price of our common stock
    appreciates.
    ITEM 1B.
    UNRESOLVED
    STAFF COMMENTS   30




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ITEM 2.
    PROPERTIES    Approximate




ExpirationLocation

Square Footage


Use

DateOne Gateway Center, Suite 702 
    Newton, Massachusetts


6,700


Corporate office


8/31/20115 Science Park
    New Haven, Connecticut


29,300


Office and laboratory


1/11/2010310
    4th Street,

    NE
    Charlottesville, Virginia


2,600


Office


5/31/20091630-1670
    Discovery Drive
    Charlottesville, Virginia


3,700


Laboratory


10/31/201094B Industrial Road
    Troy, Virginia


1,000


Laboratory


5/31/2010     ITEM 3.
    LEGAL
    PROCEEDINGS    ITEM 4.
    SUBMISSION
    OF MATTERS TO A VOTE OF SECURITY HOLDERS   PART II  ITEM 5.
    MARKET
    FOR REGISTRANTS COMMON EQUITY, RELATED STOCKHOLDER MATTERS
    AND ISSUER PURCHASES OF EQUITY SECURITIES  Market
    Information
    Sales PricesHigh


LowFiscal Year Ended March 31, 2009First Quarter

$
19.68


$
14.25Second Quarter

$
19.59


$
12.74Third Quarter

$
16.46


$
7.15Fourth Quarter

$
11.93


$
6.38Fiscal Year Ended March 31, 2008(1)First Quarter

$
16.19


$
13.00Second Quarter

$
26.99


$
13.25Third Quarter

$
28.90


$
19.83Fourth Quarter

$
23.26


$
15.34  31




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(1)
    
    The prices for the quarters ended before October 1, 2007
    have been adjusted to reflect the
    3-for-2
    stock split effected on that date.  Holders
    of Common Stock
    Dividends
   32




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Price
    Performance
    Comparison
    of 5 Year Cumulative Total Return
 Assumes Initial Investment of $100
  
  Company/NASDAQ Stock Market/Nasdaq Biotechnology
    Index


3/31/2004



3/31/2005



3/31/2006



3/31/2007



3/31/2008



3/31/2009CLINICAL DATA



100.00




126.48




158.50




160.34




214.94




125.14NASDAQ Stock Market (US and International securities)



100.00




100.91




119.18




124.21




117.74




63.68NASDAQ Biotechnology Index



100.00




83.61




108.11




99.85




100.36




87.75   ITEM 6.
    SELECTED
    CONSOLIDATED FINANCIAL DATA  Form 10-K. Form 10-K,
  Recent Acquisitions Affecting the Comparability of the
    Selected Consolidated Financial Data
    Acquiree

Date of AcquisitionGenaissance Pharmaceuticals, Inc.

October 6, 2005Epidauros Biotechnologie A.G.

August 23, 2007Adenosine Therapeutics

August 4, 2008    33




---



##### Table of Contents



Years Ended March 31,2009


2008


2007


2006


2005(In thousands, except per share amounts)Consolidated Statements of Operations DataRevenues

$
10,442


$
5,107


$
3,828


$
1,660


$
Cost of revenues


6,489



2,627



2,240



3,045



Gross profit


3,953



2,480



1,588



(1,385
)


OPERATING EXPENSES:Research and development


44,134



16,889



9,265



2,797



Sales and marketing


7,764



3,612



1,210



408



General and administrative


19,730



16,806



14,959



6,919



863Purchased in-process research and development


55,100











36,300



Total operating expenses


126,728



37,307



25,434



46,424



863Operating loss


(122,775
)


(34,827
)


(23,846
)


(47,809
)


(863
)Interest expense


(1,802
)


(76
)


(220
)


(228
)


(31
)Interest income


716



2,020



323



61



2Other income (expense), net


179



305



210



(59
)


10Loss from continuing operations before taxes


(123,682
)


(32,578
)


(23,533
)


(48,035
)


(882
)Benefit from (provision for) income taxes






230



(233
)


(102
)


Loss from continuing operations


(123,682
)


(32,348
)


(23,766
)


(48,137
)


(882
)Income (loss) from discontinued operations, net of taxes


(8,756
)


(2,982
)


(13,756
)


(2,744
)


4,277Net (loss) income


(132,438
)


(35,330
)


(37,522
)


(50,881
)


3,395Preferred stock dividend










(104
)


(97
)


Net (loss) income applicable to common stockholders

$
(132,438
)

$
(35,330
)

$
(37,626
)

$
(50,978
)

$
3,395Loss (income) per basic and diluted share:Continuing operations

$
(5.63
)

$
(1.69
)

$
(1.68
)

$
(5.39
)

$
(0.13
)Discontinued operations


(0.40
)


(0.16
)


(0.97
)


(0.30
)


0.65Net (loss) income

$
(6.03
)

$
(1.85
)

$
(2.65
)

$
(5.69
)

$
0.52Cash dividends paid per common share

$



$



$



$
0.04


$
0.07Weighted average shares:Basic and diluted


21,962



19,081



14,186



8,953



6,584   As of March 31,2009


2008


2007


2006


2005(In thousands)Consolidated Balance Sheet Data:Cash, cash equivalents and marketable securities

$
56,355


$
67,480


$
14,071


$
7,225


$
4,171Total assets


120,917



129,448



87,490



109,789



41,130Long-term obligations


63,123



5,122



3,236



7,345



Stockholders equity


29,412



106,075



50,720



59,789



23,809  34




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##### Table of Contents



ITEM 7.
    MANAGEMENTS
    DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF
    OPERATIONS  You should read the following discussion and analysis of
    financial condition and results of operations together with the
    Selected Consolidated Financial Data included in
    Item 6 above and our consolidated financial statements and
    related notes appearing elsewhere in this Annual Report on
    Form 10-K.
    In addition to historical financial information, the following
    discussion contains forward-looking statements within the
    meaning of the Private Securities Litigation Reform Act of 1995,
    as amended, and within the meaning of Section 27A of the
    Securities Act of 1933, as amended, that reflect our plans,
    estimates and beliefs. Our actual results could differ
    materially from those discussed in the forward-looking
    statements. Factors that could cause or contribute to these
    differences include those discussed below and elsewhere in this
    document, particularly in the section entitled Risk
    Factors.
  Readers are cautioned that any forward-looking statements
    involve known and unknown risks, uncertainties and other factors
    which may cause our actual results, performance or achievements
    to be materially different from any future results, performance
    or achievements expressed or implied by such forward-looking
    statements. The forward-looking statements in this Annual Report
    on
    Form 10-K
    are subject to risks, uncertainties and assumptions including,
    among other things:
  
    our ability to raise the necessary capital to fund our
    operations and to develop and commercialize our products;
    our ability to successfully design and conduct our planned
    clinical trials;
    our ability to achieve expected synergies and operating
    efficiencies in our acquisitions, and to successfully integrate
    the operations, business and technology obtained in our
    acquisitions;
    general economic and business conditions in our markets;
    the impact of current, pending or future legislation and
    regulation of our businesses in the United States and abroad;
    our expectations and estimates concerning future financial
    performance, financing plans and the impact of competition;
    and
    the impact of technological developments and competition.  In light of these risks and uncertainties, the
    forward-looking events and circumstances discussed in this
    Annual Report on
    Form 10-K
    might not occur. We undertake no obligation to publicly update
    or revise any forward-looking statements made herein because of
    new information, future events or otherwise.
  Overview
  first-in-class best-in-category
     35




---



##### Table of Contents



Therapeutics:
  Vilazodone
  1A in vitro In
    vitro 1A 1A Journal of Medicinal Chemistry 47:
    4684-4692,
    2004 1A Journal of Clinical
    Psychopharmacology 19(3):
    268-71,
    1999
      Stedivaze
  2A best-in-category
    Other
    Therapeutic Products
  and/or 2B
 36




---



##### Table of Contents



2A
  2A
  in vitro
  Genetic
    Tests
  FAMILION
  FAMILION FAMILION FAMILION FAMILION in-network FAMILION FAMILION
  Financial
    Operations Overview
  Revenue.
  Cost of Revenue.
  Sales and Marketing Expense.
 37




---



##### Table of Contents



Research and Development Expense.
  General and Administrative Expense.
  Purchased Research and Development
    Expense. Business Combinations,
  Interest and Other Income (Expense),
    Net.
  Critical
    Accounting Policies and Significant Judgments and
    Estimates
  Form 10-K.
  Revenue Recognition 
  Allowance for Doubtful Accounts and Contractual
    Allowances 
  Valuation of Intangibles and Goodwill 
 38




---



##### Table of Contents



Business Combinations
  Goodwill and Intangible Assets
  Accounting for the Impairment or Disposal of Long-Lived
    Assets
  Accrued Expenses 
  Income Taxes 
 39




---



##### Table of Contents



Recent
    Accounting Pronouncements
  Fair Value Measurements,
  No. 07-3, Accounting for Nonrefundable Advance Payments for Goods or
    Services to be Used in Future Research and Development
    Activities, EITF 07-3. EITF 07-3 EITF 07-3 states EITF 07-3
  No. 07-1, Accounting for Collaborative Arrangements, EITF 07-1. EITF 07-1 EITF 07-1 EITF 07-1
  Business Combinations,
  EITF 07-5, Determining Whether an Instrument (or an Embedded Feature) Is
    Indexed to an Entitys Own Stock (EITF 07-5). EITF 07-5 EITF 07-5 EITF 07-5 EITF 07-5
  FAS 157-4, Determining Fair Value when the Volume and Level of Activity
    for the Asset or Liability have Significantly Decreased and
    Identifying Transactions that are not Orderly
 40




---



##### Table of Contents



FAS 115-2 FAS 124-2, Recognition and Presentation of Other-than-Temporary
    Impairments FAS 107-1 28-1, Interim Disclosures about Fair Value of Financial
    Instruments FSP 107-2 28-1 Disclosures about Fair
    Value of Financial Instruments
  Results
    of Operations
  Fiscal
    Year Ended March 31, 2009 Compared to Fiscal Year Ended
    March 31, 2008
  Revenue.
  Gross Profit.
  Research and Development Expense.
  Sales and Marketing Expense.
  General and Administrative Expense.
 41




---



##### Table of Contents



Purchased In-Process Research and Development
    Expense.
  Interest and Other Income (Expense),
    Net.
  Fiscal
    Year Ended March 31, 2008 Compared to Fiscal Year Ended
    March 31, 2007
  Revenue.
  Gross Profit.
  Research and Development Expense.
  Sales and Marketing Expense.
 42




---



##### Table of Contents



General and Administrative Expense.
  Interest and Other Income (Expense),
    Net.
  Liquidity
    and Capital Resources
    Year End March 31,2009


2008


2007(In thousands)Cash (used in) provided by:Operating activities

$
(60,250
)

$
(24,532
)

$
(12,874
)Investing activities


(7,074
)


(5,190
)


753Financing activities


69,885



69,984



18,447Effect of exchange rate


(2,136
)


422



520Increase in cash and cash equivalents

$
425


$
40,684


$
6,846     
    In February 2009, we completed a $50.0 million convertible
    debt financing.
    In October 2008 concurrent with the Avalon merger agreement, we
    entered into the following transactions with Avalon:  
    Purchased 3.4 million shares of Avalons common stock
    for $237,000;
    Entered into a royalty free, fully-paid, worldwide, perpetual,
    irrevocable, sub-licensable, exclusive license agreement to use
    the AvalonRx platform for a one-time access fee of
    $1.0 million; and
    Funded a $4.0 million term loan payable May 31, 2009,
    as amended.  
    In September 2008, we sold approximately 1.5 million shares
    of our common stock for net proceeds of $25.0 million.
    In August 2008, we acquired Adenosine Therapeutic for
    approximately $10.7 million in cash, net of $301,000
    purchase price adjustment.   43




---



##### Table of Contents



Payments
    Due by Period
  Fiscal 2011


Fiscal 2013through


through


AfterTotal


Fiscal 2010


Fiscal 2012


Fiscal 2014


Fiscal 2014(In thousands)Contractual Obligations(1):Short and long-term debt(2)

$
116,517


$
12,602


$
22,669


$
16,666


$
64,580Capital lease obligations(2)


1,048



804



229



15



Operating lease obligations


1,264



998



266







Total contractual cash obligations

$
118,829


$
14,404


$
23,164


$
16,681


$
64,580     (1)
    
    Excludes the obligations of our Cogenics segment, which was sold
    on April 14, 2009(2)
    
    Includes interest expense          Off-Balance
    Sheet Arrangements
    ITEM 7A.
    QUANTITATIVE
    AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK    Interest
    Rate Risk
    Auction
    Rate Preferred Securities
   44




---



##### Table of Contents



ITEM 8.
    FINANCIAL
    STATEMENTS AND SUPPLEMENTARY DATA  Form 10-K Page F-1.
  ITEM 9.
    CHANGES
    IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND
    FINANCIAL STATEMENT DISCLOSURE    ITEM 9A.
    CONTROLS
    AND PROCEDURES  (a)
    Evaluation
    of Disclosure Controls and Procedures.  Rule 13a-15 ,
  (b)
    Managements
    Annual Report on Internal Control Over Financial
    Reporting  Rule 13a-15(f)
       45




---



##### Table of Contents



Internal Control  Integrated
    Framework
    Changes
    in Internal Controls
  Rules 13a-15(f) 15d-15(f)
 46




---



##### Table of Contents



REPORT OF
    INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
      Internal Control  Integrated Framework
        Internal Control  Integrated Framework
     
    47




---



##### Table of Contents



ITEM 9B.
    OTHER
    INFORMATION   PART III  ITEM 10.
    DIRECTORS,
    EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE    ITEM 11.
    EXECUTIVE
    COMPENSATION    ITEM 12.
    SECURITY
    OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND
    RELATED STOCKHOLDER MATTERS    ITEM 13.
    CERTAIN
    RELATIONSHIPS AND RELATED TRANSACTIONS AND DIRECTORS
    INDEPENDENCE    ITEM 14.
    PRINCIPAL
    ACCOUNTANT FEES AND SERVICES   PART IV  ITEM 15.
    EXHIBITS,
    FINANCIAL STATEMENT SCHEDULES  Consolidated Financial Statements
    Consolidated Financial Statement
    Schedules
    Exhibits
   48




---



##### Table of Contents



SIGNATURES      
        
          
       
      49




---



##### Table of Contents



50




---



##### 



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  INDEX TO
    CONSOLIDATED FINANCIAL STATEMENTS
   
 Consolidated Financial Statements

PageReport of Independent Registered Public
    Accounting Firm


F-2Consolidated Balance Sheets at March 31,
    2009 and 2008


F-3Consolidated Statements of Operations for the
    Years Ended March 31, 2009, 2008 and 2007


F-4Consolidated Statements of Stockholders
    Equity for the Years Ended March 31, 2009, 2008 and 2007


F-5Consolidated Statements of Cash Flows for the
    Years Ended March 31, 2009, 2008 and 2007


F-6Notes to Consolidated Financial Statements


F-8   F-1




---



##### Table of Contents



REPORT
    OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM              Internal Control  Integrated Framework
   
    F-2




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    BALANCE SHEETS  March 31,2009


2008(In thousands, except share and per share amounts)ASSETSCurrent Assets:Cash and cash equivalents

$
55,180


$
54,755Marketable securities, at fair value


1,175



Accounts receivable, net


2,471



1,243Prepaid expenses and other current assets


1,240



678Assets of discontinued operations


18,541



6,903Total current assets


78,607



63,579Marketable securities, at fair value






12,725Property, plant and equipment, net


2,942



1,978Goodwill


29,496



29,496Intangible assets, net


4,747



5,353Other assets, net


4,405



257Assets of discontinued operations






16,060TOTAL ASSETS

$
120,197


$
129,448LIABILITIES AND STOCKHOLDERS EQUITYCurrent Liabilities:Current portion of long-term debt

$
6,337


$
816Current portion of capital leases


730



138Accounts payable


5,562



3,354Accrued expenses


6,131



4,421Liabilities of discontinued operations


8,902



9,522Total current liabilities


27,662



18,251Long-Term Liabilities:Long-term debt, net of current portion


46,832



1,740Capital lease obligations, net of current portion


226



445Other long-term liabilities


26



26Contingent acquisition costs (Note 3)


16,039



Liabilities of discontinued operations






2,911Total long-term liabilities


63,123



5,122Commitments and contingencies (Note 9)Stockholders Equity:Preferred Stock, $.01 par value, 1,500,000 shares
    authorized; none issued and outstanding respectively






Common stock, $.01 par value, 60,000,000 shares
    authorized; 22,742,000 and 21,151,000 shares issued at
    March 31, 2009 and 2008, respectively; 22,742,000 and
    21,136,000 shares outstanding at March 31, 2009 and
    2008, respectively


227



212Additional paid-in capital


276,788



221,059Accumulated deficit


(251,204
)


(118,766
)Treasury stock, -0- and 15,000 shares held in treasury at
    March 31, 2009 and 2008, respectively






(47
)Accumulated other comprehensive income


3,601



3,617Total stockholders equity


29,412



106,075TOTAL LIABILITIES AND STOCKHOLDERS EQUITY

$
120,197


$
129,448    F-3




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    STATEMENTS OF OPERATIONS  Years Ended March 31,2009


2008


2007(In thousands, except share and pershare amounts)Revenues

$
10,442


$
5,107


$
3,828Cost of revenues


6,489



2,627



2,240Gross profit


3,953



2,480



1,588OPERATING EXPENSES:Research and development


44,134



16,889



9,265Sales and marketing


7,764



3,612



1,210General and administrative


19,730



16,806



14,959Purchased in-process research and development


55,100







Total operating expenses


126,728



37,307



25,434Operating loss


(122,775
)


(34,827
)


(23,846
)Interest expense


(1,802
)


(76
)


(220
)Interest income


716



2,020



323Other income, net


179



305



210Loss from continuing operations before taxes


(123,682
)


(32,578
)


(23,533
)Benefit from (provision for) income taxes






230



(233
)Loss from continuing operations


(123,682
)


(32,348
)


(23,766
)Loss from discontinued operations, net of taxes


(8,756
)


(2,982
)


(13,756
)Net loss


(132,438
)


(35,330
)


(37,522
)Preferred stock dividend










(104
)Net loss applicable to common stockholders

$
(132,438
)

$
(35,330
)

$
(37,626
)Loss per basic and diluted share:Continuing operations

$
(5.63
)

$
(1.69
)

$
(1.68
)Discontinued operations


(0.40
)


(0.16
)


(0.97
)Net loss

$
(6.03
)

$
(1.85
)

$
(2.65
)Weighted average shares:Basic and diluted


21,962



19,081



14,186     F-4




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    STATEMENTS OF STOCKHOLDERS EQUITY

FOR THE
    YEARS ENDED MARCH 31, 2009, 2008 AND 2007  Common














AccumulatedPreferred


Preferred


Common


Stock


Additional











OtherStock


Stock Par


Stock


Par


Paid-in


Accumulated


Treasury


Deferred


Comprehensive





ComprehensiveShares


Value


Shares


Value


Capital


Deficit


Stock


Compensation


Income


Total


Loss(In thousands)BALANCE at April 1, 2006


234


$
2



12,780


$
128


$
105,102


$
(45,810
)

$
(47
)

$
(318
)

$
732


$
59,789Conversion of Series A preferred stock into common stock


(50
)






75



1



(1
)


















Adoption of FAS 123R


















(318
)










318







Exercise of stock options










153



1



574



















575Private placement of equity, net of transaction costs of $63










1,560



16



16,840



















16,856Exercise of stock warrants










286



3



3,702



















3,705Dividends accrued on preferred stock






















(104
)














(104
)Common stock issued for Merck license










154



1



1,622



















1,623Purchase of treasury stock


























(234
)










(234
)Retirement of treasury stock










(24
)






(234
)






234











Issuance of warrants


















120



















120Equity issued in connection with acquisitions










23







347



















347Stock-based compensation










26







4,631



















4,631Translation adjustment


































934



934


$
934Net loss






















(37,522
)














(37,522
)


(37,522
)Total comprehensive loss









































$
(36,588
)BALANCE at March 31, 2007


184



2



15,033



150



132,385



(83,436
)


(47
)






1,666



50,720Conversion of Series A preferred stock into common stock


(184
)


(2
)


276



3



(1
)


















Exercise of stock options










199



2



1,751



















1,753Exercise of stock warrants










162



2



2,561



















2,563Issuance of common stock, net of transaction costs of
    $4.5 million










5,175



52



71,312



















71,364Common stock issued for Merck license










135



1



3,618



















3,619Conversion of convertible debt










140



2



2,335



















2,337Stock-based compensation










31







6,985



















6,985Other


















113



















113Translation adjustment


































2,451



2,451


$
2,451Unrealized loss on marketable securities


































(500
)


(500
)


(500
)Net loss






















(35,330
)














(35,330
)


(35,330
)Total comprehensive loss









































$
(33,379
)BALANCE at March 31, 2008










21,151



212



221,059



(118,766
)


(47
)






3,617



106,075Exercise of stock options










38







209



















209Exercise of stock warrants










17



























Issuance of common stock and warrants, net of transaction costs
    of $36










1,515



15



24,949



















24,964Warrants issued in connection with the convertible notes


















10,767



















10,767Beneficial conversion feature of the convertible notes


















10,428



















10,428Retirement of treasury stock










(15
)






(47
)






47











Stock-based compensation










36







9,423



















9,423Translation adjustment


































(1,838
)


(1,838
)

$
(1,838
)Unrealized gain on marketable securities


































1,822



1,822



1,822Net loss






















(132,438
)            -














(132,438
)


(132,438
)Total comprehensive loss









































$
(132,454
)BALANCE at March 31, 2009





$




22,742


$
227


$
276,788


$
(251,204
)

$



$



$
3,601


$
29,412    F-5




---



##### Table of Contents





CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    STATEMENTS OF CASH FLOWS  Years Ended March 31,2009


2008


2007(In thousands)CASH FLOWS FROM OPERATING ACTIVITIES:Net loss

$
(132,438
)

$
(35,330
)

$
(37,522
)Less loss from discontinued operations


8,756



2,982



13,756Loss from continuing operations


(123,682
)


(32,348
)


(23,766
)Adjustments to reconcile loss from continuing operations to net
    cash used in operating activities:Depreciation and amortization


1,670



673



539Purchased in-process research and development


55,100







Stock-based compensation including Merck license


8,130



9,523



4,702Accretion of discount on convertible note


106







Loss on sales of equipment


51



10



Changes in current assets and liabilities, net of acquired
    assets and liabilities:Accounts receivable


(1,228
)


(323
)


(176
)Prepaid expenses and other current assets


(553
)


(319
)


157Other assets


155



(229
)


41Accounts payable and accrued expenses


3,664



4,522



(446
)Other liabilities


(2
)






Cash used in continuing operations


(56,589
)


(18,491
)


(18,949
)Cash (used in) provided by discontinued operations


(3,661
)


(6,041
)


6,075Net cash used in operating activities


(60,250
)


(24,532
)


(12,874
)CASH FLOWS FROM INVESTING ACTIVITIES:Purchases of equipment


(1,241
)


(511
)


(241
)Proceeds from sales of equipment






84



Purchases of marketable securities






(15,275
)


Proceeds from sale of marketable securities


12,050



2,050



Cash used in business combinations, net of cash acquired


(16,850
)


(11,997
)


(222
)Cash used in investing activities  continuing
    operations


(6,041
)


(25,649
)


(463
)Cash (used in) provided by investing activities 
    discontinued operations


(1,033
)


20,459



1,216Net cash (used in) provided by investing activities


(7,074
)


(5,190
)


753      F-6




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  Years Ended March 31,2009


2008


2007(In thousands)CASH FLOWS FROM FINANCING ACTIVITIES:Borrowings under other debt arrangements


50,000







18Payment on debt and capital leases


(3,703
)


(413
)


(589
)Proceeds from the sale of common stock and warrants, net of
    transaction costs


24,964



71,364



20,561Purchase of treasury shares










(234
)Exercise of stock options and warrants


209



4,316



575Cash provided by financing activities  continuing
    operations


71,470



75,267



20,331Cash (used in) provided by financing activities 
    discontinued operations


(1,585
)


(5,283
)


(1,884
)Net cash provided by financing activities


69,885



69,984



18,447EFFECT OF EXCHANGE RATE CHANGES ON CASH AND CASH EQUIVALENTS


(2,136
)


422



520NET INCREASE IN CASH AND CASH EQUIVALENTS


425



40,684



6,846CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD


54,755



14,071



7,225CASH AND CASH EQUIVALENTS, END OF PERIOD

$
55,180


$
54,755


$
14,071Supplemental disclosure of cash flow information:Cash paid during the year for:Interest

$
930


$
76


$
220Income taxes

$



$



$
Non-cash investing and financing transactions:Equipment acquired through capital leases

$
307


$
567


$
279Accrued acquisition costs

$
207


$



$
Debt issued in business acquisitions

$
25,200


$



$
Equity issued to acquired technology rights

$



$
3,619


$
1,623Issuance of common stock upon note conversion

$



$
2,337


$
Warrants issued in connection with amendment of convertible note
    payable

$



$



$
120Accrued preferred stock dividends

$



$



$
146Equity issued in business acquisitions

$



$



$
219      F-7




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL STATEMENTS
 FOR THE
    YEARS ENDED MARCH 31, 2009, 2008 AND 2007
  (1)
    Nature of
    Business and Basis of Presentation  Nature
    of Business
    first-in-class best-in-class
    Basis
    of Presentation
           F-8




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        
    partnering opportunities with pharmaceutical or biotechnology
    companies for the marketing of vilazodone;
    license, sublicense, or other sources of financing relating to
    the development programs of the recently acquired Adenosine
    Therapeutics compounds
    and/or
    patents;
    sale of non-core assets; and/or
    sale of equity or debt securities.      (2)
    Significant
    Accounting Policies  Principles
    of Consolidation
   F-9




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Use
    of Estimates
    Cash
    and Cash Equivalents
    Marketable
    Securities
  available-for-sale Accounting for Certain
    Investments in Debt and Equity Securities
  Fair
    Value Measurements
    Accounts
    Receivable
      2009


2008


2007(In thousands)Allowance for uncollectible accounts  beginning of
    year

$
500


$
346


$
151Provisions


1,015



189



272Less: deductions


(223
)


(35
)


(77
)Allowance for uncollectible accounts  end of year

$
1,292


$
500


$
346  F-10




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Depreciation
    and Amortization
    Asset Classification

Useful LivesLaboratory equipment

2-7 yearsLeasehold improvements

Lesser of useful life or lease termComputer equipment

3-7 yearsFurniture and fixtures

2-7 years     Goodwill
    and Intangibles
    Goodwill and other
    Intangible Assets
  Accounting for the
    Impairment or Disposal of Long-Lived Assets
  Revenue
    Recognition
      Research
    and Development Costs
    Income
    Taxes
   F-11




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Accounting for
    Uncertainty in Income Taxes
  Comprehensive
    Loss
      March 31,2009


2008(In thousands)Foreign currency translation adjustment

$
2,279


$
4,117Unrealized loss on marketable securities






(500
)Unrealized gain on investment in Avalon


1,322



Total

$
3,601


$
3,617   Foreign
    Currency
    Loss
    per Share
   F-12




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2009


2008


2007(In thousands)Common stock options


3,630



2,539



2,010Common stock warrants


4,567



1,011



1,183Convertible note payable


6,110







134Restricted common stock










12Convertible Series A preferred stock










276Total


14,307



3,550



3,615   Equity-Based
    Compensation
    Concentration
    of Credit Risk
    Fair
    Value of Financial Instruments
        Description

Level 1


Level 2


Level 3


TotalAssets:Cash equivalents

$
37,659


$



$



$
37,659Marketable securities  ARPS










1,175



1,175Marketable securities  Avalon common stock


1,560











1,560  F-13




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Auction RateSecurities(In thousands)Balance at March 31, 2008

$
12,725ARPS redeemed at par


(12,050
)Reversal of unrealized loss recorded in other comprehensive
    income


500Balance at March 31, 2009

$
1,175   Segment
    and Geographical Information
  Disclosures About Segments of an
    Enterprise and Related Information
    Recent
    Accounting Pronouncements
    No. 07-3, Accounting for Nonrefundable Advance Payments for Goods or
    Services to be Used in Future Research and Development
    Activities (EITF 07-3). EITF 07-3 EITF 07-3 states EITF 07-3
  No. 07-1, Accounting for Collaborative Arrangements, (EITF 07-1). EITF 07-1 EITF 07-1
 F-14




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  EITF 07-1
  Business Combinations
  EITF 07-5, Determining Whether an Instrument (or an Embedded Feature) Is
    Indexed to an Entitys Own Stock (EITF 07-5). EITF 07-5 EITF 07-5 EITF 07-5 EITF 07-5
  FAS 157-4, Determining Fair Value when the Volume and Level of Activity
    for the Asset or Liability have Significantly Decreased and
    Identifying Transactions that are not Orderly FAS 115-2 FAS 124-2, Recognition and Presentation of
    Other-than-Temporary
    Impairments other-than-temporary FAS 107-1 28-1, Interim Disclosures about Fair Value of Financial
    Instruments FSP 107-2 28-1 Disclosures about Fair
    Value of Financial Instruments
  (3)
    Discontinued
    Operations   F-15




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Vital
    Diagnostics
    CDSS
    Vital
    Scientific
      Electa
    Lab
    Cogenics
   F-16




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2009


2008


2007(In thousands)Revenue

$
27,018


$
50,381


$
84,665Loss from Operations Before Disposal:Loss before taxes and minority interest

$
(8,288
)

$
(9,518
)

$
(5,436
)Minority interest










(9
)Loss before taxes


(8,288
)


(9,518
)


(5,445
)Income taxes


(216
)


(1,365
)


(1,133
)Loss from discontinued operations, net of taxes


(8,504
)


(10,883
)


(6,578
)Disposal:Loss on disposal, net of taxes


(252
)


7,901



(7,178
)Loss from discontinued operations, net of tax

$
(8,756
)

$
(2,982
)

$
(13,756
)     March 31,2009


2008(In thousands)Accounts receivable, net

$
4,832


$
5,047Prepaid expenses and other current assets


1,678



1,856Property, plant and equipment, net


5,708



7,191Goodwill


1,416



1,584Intangible assets, net


4,499



6,764Other assets


408



521Assets of discontinued operations

$
18,541


$
22,963Current portion of capital leases and long-term debt

$
1,397


$
1,609Accounts payable


1,731



2,779Other accrued expenses


2,248



2,878Customer advances


2,192



2,256Capital leases and long-term debt, net of current portion


1,235



2,829Other long-term liabilities


99



82Liabilities of discontinued operations

$
8,902


$
12,433   (4)
    Business
    Combinations  Adenosine
    Therapeutics, LLC
  32-month
 F-17




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Business
    Combinations
      (In thousands)Cash

$
10,699Debt


25,200Contingent acquisition costs


16,039Transaction costs


400$
52,338   (In thousands)Preliminary Purchase Price AllocationPrepaid expenses and other current assests

$
9Property and equipment


351Other assets


23Purchased in-process research and development costs


52,100Accrued vacation


(47
)Capital lease obligations


(96
)Deferred rent


(2
)Total purchase price

$
52,338    F-18




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2A best-in-category
          Year Ended March 31,2009


2008(In thousands)(Unaudited)Revenue

$
11,411


$
7,733Net loss


(134,243
)


(92,811
)Basic and diluted net loss per share

$
(6.11
)

$
(4.86
)       Avalon
    Pharmaceuticals, Inc.
   F-19




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        Private
    Placement
        Term
    Loan
     F-20




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Exclusive
    License Agreement
  ®
    (5)
    Property,
    Plant and Equipment    2009


2008(In thousands)Laboratory equipment

$
1,197


$
517Leasehold improvements


1,527



1,416Computer equipment and software


2,022



938Furniture and fixtures


187



1434,933



3,014Less: accumulated depreciation and amortization


(1,991
)


(1,036
)$
2,942


$
1,978     (6)
    Intangible
    Assets    AverageUsefulLife


2009


2008(In thousands)Completed technology


8.4 years


$
5,955


$
5,955Customer relationships


5.0 years



400



400Other


7.0 years



100



1006,455



6,455Less: accumulated amortization






(1,708
)


(1,102
)Intangible assets, net





$
4,747


$
5,353      F-21




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (7)
    Accrued
    Expenses    2009


2008(In thousands)Payroll and payroll-related expenses

$
2,020


$
2,800Project expenses


1,147



Commissions, royalties and license fees


1,063



745Other


1,901



876$
6,131


$
4,421   (8)
    Debt    2009


2008(In thousands)Notes payable, bearing interest at 6.5%, with maturities between
    February 2009 and May 2011 and secured by certain of
    PGxHealths leasehold improvements

$
2,001


$
2,556Note payable, bearing interest at 11% with monthly principal
    payments of $100 through April 1, 2011, secured by
    substantially all of the assets of the Company


2,500



Note payable, bearing interest at 6% with quarterly principal
    payments of $1,000 through July 13, 2013, secured by
    substantially all of the assets of the Company


19,800



Convertible notes payable


50,000



74,301



2,556Less: current portion


(6,337
)


(816
)unamortized discount


(21,132
)


$
46,832


$
1,740      F-22




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      2010

$
6,3372011


6,6352012


4,7292013


4,4002014


2,200After


50,000Total

$
74,301   (9)
    Commitments
    and Contingencies  Litigation
    Contractual
    Commitments and Commercial Obligations
    Operating


CapitalYear Ending March 31,

Leases


Leases2010

$
998


$
8042011


244



1302012


22



992013






152014






Thereafter






Total

$
1,264



1,048Less: amount representing interest






(92
)Total principal obligations






956Less: current portion






(730
)Long-term capital lease





$
226      F-23




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Vilazodone
    Commitments
    Adenosine
    Therapeutics Acquisition Commitments
  and/or and/or dollar-for-dollar dollar-for-dollar
  (10)
    Equity  Preferred
    Stock
    Common
    Stock
     F-24




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        (11)
    Income
    Taxes  Accounting for Income Taxes
    Jurisdiction

Tax YearsUnited States


2006-2009United Kingdom


2006-2009France


2006-2009Germany


2004-2009     2009


2008


2007(In thousands)United States

$
(124,410
)

$
(31,272
)

$
(24,805
)Foreign


728



(1,306
)


1,272$
(123,682
)

$
(32,578
)

$
(23,533
)  F-25




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2009


2008


2007(In thousands)Current:Federal

$



$
(16
)

$
Foreign






(214
)


197Total Current






(230
)


197Deferred:Federal










192Foreign










Change in valuation allowance










(156
)Total Deferred










36$



$
(230
)

$
233     2009


2008


2007(In thousands)Benefits from taxes at statutory rate

$
(42,052
)

$
(11,076
)

$
(8,001
)Stock-based compensation


2,606



1,072



750Change in valuation reserves


36,228



9,575



5,685Other


3,218



199



1,799



(230
)


233     2009


2008(In thousands)Deferred tax assets:Net operating losses

$
81,695


$
66,402Capitalized research costs


6,730



10,480Purchased intangibles


17,766



Capital losses


4,545



1,733Tax credits


2,752



295Other reserves and accrued liabilities


2,019



369Total assets


115,507



79,279Deferred tax liabilities:Purchased intangibles






(875
)Total liabilities






(875
)Net deferred tax asset


115,507



78,404Less: valuation allowance


(115,507
)


(78,404
)$



$
  F-26




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        (12)
    Stock
    Incentive Plans and Equity Based Compensation          WeightedWeighted


AverageAverage


Remaining


AggregateNumber of


Exercise


Contractual


IntrinsicShares


Price


Term


Value(In thousands, except for per share amounts)Outstanding April 1, 2008


2,539


$
14.53Granted


1,256



12.93Cancelled/Expired


(123
)


18.28Exercised


(42
)


6.71Outstanding March 31, 2009


3,630


$
13.61



8.1 years


$
1,664Exercisable March 31, 2009


1,625


$
13.56



7.0 years


$
326Exercisable March 31, 2008


936


$
14.19Available for future grants March 31, 2009


956  F-27




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        2009


2008


2007(In thousands)Cost of revenues

$
258


$
301


$
Sales and marketing


1,071



564



Research and development


1,298



523



474General and administrative


5,503



4,515



2,605Pre-tax stock based compensation expense

$
8,130


$
5,903


$
3,079Income tax benefits










Stock based compensation expense, net

$
8,130


$
5,903


$
3,079           2009

2008

2007Weighted-average interest rate

1.50 - 3.50%

2.75 - 4.75%

4.00-5.18%Expected dividend yield

0.00%

0.00%

0.00%Expected lives

6 years

6 years

5 - 6 yearsExpected volatility

65 - 69%

71 - 79%

73 - 82%Forfeiture rate

5.00%

0.00%

0.00%Weighted average grant date fair value

$7.96

$12.30

$6.89  F-28




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (13)
    Defined
    Contribution Plans    (14)
    Related
    Party Transactions                 F-29




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    (15)
    Quarterly
    Summarized Financial Information (Unaudited)    Fiscal year ended March 31, 20091st Quarter


2nd Quarter(1)


3rd Quarter


4th Quarter(In thousands, except per share amounts)Net revenue

$
2,037


$
2,400


$
2,781


$
3,224Gross profit


564



856



964



1,567Operating loss


(12,806
)


(67,438
)


(22,203
)


(20,328
)Loss from continuing operations


(12,526
)


(67,276
)


(22,403
)


(21,477
)Income (loss) from discontinued operations


(2,338
)


(2,734
)


(1,275
)


(2,409
)Net loss


(14,864
)


(70,010
)


(23,678
)


(23,886
)Net loss per basic and diluted share:Continuing operations

$
(0.59
)

$
(3.17
)

$
(0.98
)

$
(0.94
)Discontinued operations

$
(0.11
)

$
(0.13
)

$
(0.06
)

$
(0.11
)   Fiscal year ended March 31, 20081st Quarter


2nd Quarter


3rd Quarter


4th Quarter(In thousands, except per share amounts)Net revenue

$
950


$
1,137


$
1,428


$
1,592Gross profit


551



767



356



806Operating loss


(3,924
)


(6,668
)


(12,471
)


(11,764
)Loss from continuing operations


(3,882
)


(5,678
)


(11,796
)


(10,992
)Income (loss) from discontinued operations


(1,531
)


(5,204
)


7,447



(3,694
)Net loss


(5,413
)


(10,882
)


(4,349
)


(14,686
)Net loss per basic and diluted share:Continuing operations

$
(0.26
)

$
(0.30
)

$
(0.56
)

$
(0.52
)Discontinued operations

$
(0.11
)

$
(0.27
)

$
0.36


$
(0.18
)     (1)
    
    The operating loss for the quarter ended September 30, 2008
    includes $52.1 million related to inprocess research and
    development expense arising from the acquisition of Adenosine
    Therapeutics. F-30




---



##### Table of Contents



EXHIBIT INDEX
  ExhibitNumber

Description2
.1

Agreement and Plan of Merger, dated as of June 20, 2005,
    among Clinical Data, Safari Acquisition Corporation and
    Genaissance Pharmaceuticals, Inc. Filed as Exhibit 2.1 to
    the Companys Current Report on
    Form 8-K,
    as filed with the Commission on June 28, 2005, and
    incorporated herein by reference.2
.2

First Amendment to Agreement and Plan of Merger, dated as of
    July 28, 2005, among Clinical Data, Safari Acquisition
    Corporation and Genaissance Pharmaceuticals, Inc. Filed as
    Exhibit 2.1 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on August 2, 2005, and
    incorporated herein by reference.2
.3

Agreement and Plan of Merger and Reorganization, dated as of
    October 27, 2008, by and among Clinical Data, Inc., API
    Acquisition Sub II, LLC and Avalon Pharmaceuticals, Inc. Filed
    as Exhibit 99.1 to Clinical Datas Current Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.2
.4

First Amendment to the Agreement and Plan of Merger and
    Reorganization, dated January 12, 2009, between Clinical
    Data, Inc., API Acquisition Sub II, LLC and Avalon
    Pharmaceuticals, Inc. Filed as Exhibit 2.2 to the
    Companys Registration Statement on
    Form S-4/A
    (File
    No. 333-156011),
    filed with the Commission on January 13, 2009, and
    incorporated herein by reference.2
.5

Second Amendment to the Agreement and Plan of Merger and
    Reorganization, dated March 30, 2009, between Clinical
    Data, Inc., API Acquisition Sub II, LLC and Avalon
    Pharmaceuticals, Inc. Filed as Exhibit 10.9 to the
    Companys Registration Statement on
    Form S-4/A
    (File
    No. 333-156011),
    filed with the Commission on April 2, 2009, and
    incorporated herein by reference.2
.6

Stock Purchase Agreement, dated April 1, 2009, among
    Clinical Data, Inc., Clinical Data B.V., Beckman Coulter, Inc.,
    Beckman Coulter GmbH, and Beckman Coulter Holdings GmbH. Filed
    as Exhibit 2.1 to the Companys Current Report on
    Form 8-K/A,
    filed with the Commission on April 27, 2009, and
    incorporated herein by reference.3
.1

Restated Certificate of Incorporation filed with the Secretary
    of State of the State of Delaware on June 11, 2008. Filed
    as Exhibit 3.2 to the Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 16, 2008, and
    incorporated herein by reference.3
.2

Amended and Restated By-laws of the Company, as of June 20,
    2005. Filed as Exhibit 3.1 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on June 24, 2005, and
    incorporated herein by reference.4
.1

Specimen Common Stock Certificate. Filed as Exhibit 4.1 to
    the Companys Registration Statement on
    Form S-1
    (File
    No. 2-82494),
    as filed with the Commission on March 17, 1983, and
    incorporated herein by reference.4
.2

Specimen Certificate of Contingent Value Rights to receive
    common stock. Filed herewith.10
.1

2002 Incentive and Stock Plan. Filed as Exhibit A to the
    Companys Proxy Statement on Schedule 14A filed with
    the Commission on July 29, 2002, and incorporated herein by
    reference.10
.2

Form of Incentive Stock Option Certificate under the 2002 Equity
    Incentive and Stock Plan for all U.S. employees, including
    executive officers. Filed as Exhibit 10.5 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on November 14, 2005, and
    incorporated herein by reference.10
.3

Form of Non-Statutory Stock Option Certificate under the 2002
    Incentive and Stock Plan for all U.S. employees, including
    executive officers. Filed as Exhibit 10.6 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on November 14, 2005, and
    incorporated herein by reference.10
.4

Amended and Restated 2005 Equity Incentive Plan. Filed as
    Exhibit 10.1 to the Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on November 14, 2007, and
    incorporated herein by reference.10
.5

Form of Stock Option Grant Notice and Stock Option Agreement
    under the Companys 2005 Equity Incentive Plan for all U.S.
    employees, including executive officers, and directors. Filed as
    Exhibit 10.6 to the Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 29, 2006, and
    incorporated herein by reference.10
.6*

Executive Employment Agreement of Andrew J. Fromkin effective as
    of May 12, 2006. Filed as Exhibit 99.2 to the
    Companys Current Report on
    Form 8-K/A,
    filed with the Commission on November 13, 2006, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description10
.7*

Executive Employment Agreement of Caesar J. Belbel effective as
    of May 12, 2006. Filed as Exhibit 99.3 to the
    Companys Current Report on
    Form 8-K/A,
    filed with the Commission on November 13, 2006, and
    incorporated herein by reference.10
.8*

Executive Employment Agreement of C. Evan Ballantyne effective
    as of June 16, 2008. Filed as Exhibit 10.8 to the
    Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 16, 2008, and
    incorporated herein by reference.10
.9*

Form of Amended and Restated Indemnification Agreement between
    the Company and Arthur Malman. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on July 11, 2005, and
    incorporated herein by reference.10
.10*

Form of Indemnification Agreement between the Company and
    certain executive officers and directors of the Company. Filed
    as Exhibit 99.2 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on July 11, 2005, and
    incorporated herein by reference.10
.11*

Amended and Restated Executive Employment Agreement of Carol R.
    Reed, M.D. effective as of June 16, 2008. Filed as
    Exhibit 10.1 to the Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on August 11, 2008, and
    incorporated herein by reference.10
.12

Form of Common Stock Purchase Warrant issued in connection with
    the Securities Purchase Agreement, dated as of November 17,
    2005. Filed as Exhibit 99.2 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on November 21, 2005, and
    incorporated herein by reference.10
.13

Form of Registration Rights Agreement among the Company and the
    Investors listed therein, dated as of November 17, 2005.
    Filed as Exhibit 99.3 to the Companys Current Report
    on
    Form 8-K,
    filed with the Commission on November 21, 2005, and
    incorporated herein by reference.10
.14

Form of Common Stock Purchase Warrant issued in connection with
    the Securities Purchase Agreement, dated as of June 13,
    2006. Filed as Exhibit 99.2 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on June 15, 2006, and
    incorporated herein by reference.10
.15

Form of Registration Rights Agreement among the Company and the
    Investors, dated as of June 13, 2006. Filed as
    Exhibit 99.3 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on June 15, 2006, and
    incorporated herein by reference.10
.16

Asset Purchase Agreement, dated August 4, 2008, by and
    among PGxHealth, LLC and Adenosine Therapeutics, L.L.C. Filed as
    Exhibit 99.1 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on August 8, 2008, and
    incorporated herein by reference.10
.17

Share Purchase Agreement, dated as of August 23, 2007,
    among Clinical Data, Inc., Clinical Data B.V, and the
    stockholders of Epidauros Biotechnologie AG. Filed as
    Exhibit 99.1 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on August 29, 2007, and
    incorporated herein by reference.10
.18

Stock Purchase Agreement, dated as of October 25, 2007,
    among Clinical Data, Inc., Clinical Data B.V, Financiere Elitech
    S.A.S. and Elitech Holding B.V. Filed as Exhibit 99.2 to
    the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 30, 2007, and
    incorporated herein by reference.10
.19

Secured Promissory Note (Principal Amount $22,000,000), dated
    August 4, 2008, among PGxHealth, LLC and Adenosine
    Therapeutics, LLC. Filed as Exhibit 99.2 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on August 8, 2008, and
    incorporated herein by reference.10
.20

Secured Promissory Note (Principal Amount $3,200,000), dated
    August 4, 2008, among PGxHealth, LLC and Adenosine
    Therapeutics, LLC. Filed as Exhibit 99.3 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on August 8, 2008, and
    incorporated herein by reference.10
.21

Security Agreement, dated as of August 4, 2008, among
    PGxHealth, LLC and Adenosine Therapeutics, LLC. Filed as
    Exhibit 99.4 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on August 8, 2008, and
    incorporated herein by reference.10
.22

Guaranty, dated as of August 4, 2008, among the Company and
    Adenosine Therapeutics, LLC. Filed as Exhibit 99.5 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on August 8, 2008, and
    incorporated herein by reference.10
.23

Express CreditLine Revolving Loan Agreement and Amendment to
    Express CreditLine or Express Credit Loan Agreement, each dated
    September 17, 2008. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on September 23, 2008, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description10
.24

Form of Securities Purchase Agreement, dated September 26,
    2008, among Clinical Data, Inc. and Purchasers as listed
    therein. Filed as Exhibit 99.1 to the Companys
    Current Report on
    Form 8-K,
    filed with the Commission on September 30, 2008, and
    incorporated herein by reference.10
.25

Form of Registration Rights Agreement, dated September 26,
    2008, among Clinical Data, Inc. and Purchasers as listed
    therein. Filed as Exhibit 99.2 to the Companys
    Current Report on
    Form 8-K,
    filed with the Commission on September 30, 2008, and
    incorporated herein by reference.10
.26

Form of Common Stock Purchase Warrant, dated September 26,
    2008. Filed as Exhibit 99.3 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on September 30, 2008, and
    incorporated herein by reference.10
.27

Voting Agreement, dated October 27, 2008 (separate Voting
    Agreements have been entered into between Clinical Data, Inc.
    and each of the following Avalon Pharmaceuticals, Inc.
    stockholders: J. Michael Hamilton, Stephen K. Horrigan, Kenneth
    C. Carter, David S. Kabakoff, Bradley G. Lorimier, Philip Frost,
    C. Eric Winzer, Michael R. Kurman, and William H. Washecka).
    Form filed as Exhibit 99.3 to Clinical Datas Current
    Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.28

Securities Purchase Agreement, dated October 27, 2008,
    between Clinical Data, Inc. and Avalon Pharmaceuticals, Inc.
    Filed as Exhibit 99.4 to Clinical Datas Current
    Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.29

Common Stock Purchase Warrant issued by Avalon Pharmaceuticals,
    Inc. to Clinical Data, Inc. Filed as Exhibit 99.5 to
    Clinical Datas Current Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.30

Contingent Value Rights Agreement, dated May 28, 2009,
    among Clinical Data, Inc. and America Stock Transfer and
    Trust Co. Filed as Exhibit 99.2 to Clinical
    Datas Current Report on
    Form 8-K,
    filed with the Commission on June 3, 2009, and incorporated
    herein by reference.10
.31

Letter Agreement, dated November 17, 2008, between Clinical
    Data, Inc. and Avalon Pharmaceuticals, Inc. Filed as
    Exhibit 10.3B to the Companys Registration Statement
    on
    Form S-4
    (Registration
    No. 333-156011),
    filed with the Commission on December 9, 2008, and
    incorporated herein by reference.10
.32

License Agreement, dated October 27, 2008, between Clinical
    Data, Inc. and Avalon Pharmaceuticals, Inc. Filed as
    Exhibit 99.7 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.33

Note Purchase Agreement, dated October 27, 2008, between
    Clinical Data, Inc. and Avalon Pharmaceuticals, Inc. Filed as
    Exhibit 99.8 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.34

Term Note, dated October 27, 2008, issued by Avalon
    Pharmaceuticals, Inc. to Clinical Data, Inc. Filed as
    Exhibit 99.9 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.10
.35

Amendment No. 1 to Term Note, dated January 12, 2009,
    issued by Avalon Pharmaceuticals, Inc. to Clinical Data, Inc.
    Filed as Exhibit 10.7 to Amendment No. 1 to the
    Companys Registration Statement on
    Form S-4/A
    (File
    No. 333-156011),
    filed with the Commission on January 13, 2009, and
    incorporated herein by reference.10
.36

Amendment No. 2 to Term Note, dated March 30, 2009,
    issued by Avalon Pharmaceuticals, Inc. to Clinical Data, Inc.
    Filed as Exhibit 10.9 to Amendment No. 2 to the
    Companys Registration Statement on
    Form S-4/A
    (File
    No. 333-156011),
    filed with the Commission on April 2, 2009, and
    incorporated herein by reference.10
.37

Term Note, dated March 30, 2009, issued by Avalon
    Pharmaceuticals, Inc. to Clinical Data, Inc. Filed as
    Exhibit 10.10 to the Companys Registration Statement
    on
    Form S-4/A
    (File
    No. 333-156011),
    filed with the Commission on April 2, 2009, and
    incorporated herein by reference.10
.38

Intellectual Property Security Agreement, dated October 27,
    2008, between Clinical Data, Inc. and Avalon Pharmaceuticals,
    Inc. Filed as Exhibit 99.10 to Clinical Datas Current
    Report on
    Form 8-K,
    filed with the Commission on October 31, 2008, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description10
.39

License, Development and Cooperation Agreement by and between
    Merck KGaA and Genaissance Pharmaceuticals, Inc., dated
    September 22, 2004. Filed as Exhibit 99.1 to
    Genaissances Current Report on
    Form 8-K/A,
    filed with the Commission on October 13, 2004, and
    incorporated herein by reference.10
.40

Form of Securities Purchase Agreement, dated February 25,
    2009, among Clinical Data, Inc. and Buyers listed therein. Filed
    as Exhibit 99.1 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on February 26, 2009, and
    incorporated herein by reference.10
.41

Form of Registration Rights Agreement, dated February 25,
    2009, among Clinical Data, Inc. and Buyers listed therein. Filed
    as Exhibit 99.2 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on February 26, 2009, and
    incorporated herein by reference.10
.42

Form of Note, dated February 25, 2009. Filed as
    Exhibit 99.3 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on February 26, 2009, and
    incorporated herein by reference.10
.43

Form of Common Stock Purchase Warrant (Series A), dated
    February 25, 2009. Filed as Exhibit 99.4 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on February 26, 2009, and
    incorporated herein by reference.10
.44

Form of Common Stock Purchase Warrant (Series B), dated
    February 25, 2009. Filed as Exhibit 99.5 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on February 26, 2009, and
    incorporated herein by reference.10
.45

Escrow Agreement, dated April 14, 2009, among Clinical
    Data, Inc., Beckman Coulter, Inc. and Wells Fargo, N.A. Filed as
    Exhibit 99.2 to the Companys Current Report on
    Form 8-K/A,
    filed with the Commission on April 27, 2009, and
    incorporated herein by reference.10
.46

Transition Services Agreement, dated April 14, 2009, by and
    among Clinical Data, Inc., Cogenics, Inc., Epidauros
    Biotechnologie, Aktiengesellschaft, and Cogenics Genome Express,
    S.A. Filed as Exhibit 99.3 to the Companys Current
    Report on
    Form 8-K/A,
    filed with the Commission on April 27, 2009, and
    incorporated herein by reference.10
.47

Patent License Agreement, dated April 14, 2009, by and
    between PGxHealth, LLC and Beckman Coulter, Inc. Filed as
    Exhibit 99.4 to the Companys Current Report on
    Form 8-K/A,
    filed with the Commission on April 27, 2009, and
    incorporated herein by reference.14
.1

Code of Business Conduct and Ethics. Filed as Exhibit 14.1
    to the Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 29, 2006, and
    incorporated herein by reference.21
.1

Subsidiaries of the Company. Filed herewith.23
.1

Consent of Deloitte & Touche LLP, an independent
    registered public accounting firm. Filed herewith.31
.1

Certification of Chief Executive Officer Pursuant to
    §240.13a-14 or §240.15d-14 of the Securities Exchange
    Act of 1934, as amended. Filed herewith.31
.2

Certification of Chief Financial Officer Pursuant to
    §240.13a-14 or §240.15d-14 of the Securities Exchange
    Act of 1934, as amended. Filed herewith.32
.1

Certification of Chief Executive Officer and Chief Financial
    Officer pursuant to 18 U.S.C. Section 1350. Filed
    herewith.     *
    
    Indicates a contract with management.
    
    Confidential treatment requested as to certain portions, which
    portions have been filed separately with the Commission.