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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,
    2010ORo

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, 2010
  PagePART 1ITEM 1.


Business


1ITEM 1A.


Risk Factors


14ITEM 1B.


Unresolved Staff Comments


29ITEM 2.


Properties


29ITEM 3.


Legal Proceedings


30PART IIITEM 5.


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


30ITEM 6.


Selected Consolidated Financial Data


31ITEM 7.


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


33ITEM 7A.


Quantitative and Qualitative Disclosures about
    Market Risk


43ITEM 8.


Financial Statements and Supplementary Data


43ITEM 9.


Changes in and Disagreements with Accountants on
    Accounting and Financial Disclosure


43ITEM 9A.


Controls and Procedures


43ITEM 9B.


Other Information


46PART IIIITEM 10.


Directors, Executive Officers and Corporate
    Governance


46ITEM 11.


Executive Compensation


46ITEM 12.


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


46ITEM 13.


Certain Relationships and Related Transactions,
    and Directors Independence


46ITEM 14.


Principal Accounting Fees and Services


46PART IVITEM 15.


Exhibits, Financial Statement Schedules


46SIGNATURES


47EX-21.1EX-23.1EX-31.1EX-31.2EX-32.1    ® 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. Form 10-K




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PART I  ITEM 1.
    BUSINESS  General
    1A 2A best-in-class
  first-in-human 2A 2B
  FAMILION
        Vilazodone
  1A American
 1




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Journal of Psychiatry Current Therapeutic Research
        Stedivaze
  2A
  best-in-class
   2




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. Journal of Nuclear Cardiology,
    Other
    Therapeutics in Development
  2A 2A
  and/or 2B
  2A
    Company
    History
    FAMILION
  FAMILION
 3




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##### Table of Contents



2A best-in-category
    2B
    first-in-class, best-in-category,
    OUR
    INDUSTRIES
  Therapeutic
    Development
  in vitro in vivo and/or
  Genetic
    Tests
   4




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OUR
    COMPANY
  Our
    Strategy
  best-in-class and/or first-in-class 1A 2A best-in-class first-in-human
  and/or
  Our
    Pharmaceutical Pipeline
  Vilazodone
  About
    Depression
  J Affect Disord
    2005 Jul 87 (1):43-55 American Journal of
    Psychiatry
  Current Therapeutic Research
  Market
    Opportunity and Competition
   5




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About
    Vilazodone
  1A
  Journal of Clinical
    Psychiatry
         6




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Stedivaze
  Overview
  2A best-in-class
  About
    Myocardial Perfusion Imaging
  2A Circulation 711-718].
  Market
    Opportunity and Competition
   7




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2A 1 2B 3 supra. p.7
  About
    PRX-08066
  2B
  Preclinical
    Therapeutic Development Programs
  ATL313
  2A 2A
  ATL844
  and/or 2B
  ATL1222
  2A
  AVN316
   8




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Strategic
    Acquisitions
    Our
    Genetic Tests
  FAMILION
    The
    FAMILION Family of Tests
  Sudden Arrhythmia Death
    Syndromes Foundation (SADS) citing CDC 2002
  SADS Foundation
  30-50% J Cardiovasc Electrophysiol. 2007;
    18(7):791-7
  Nature, 2008; 5(3):158-68
  Prog Cardiovasc Dis. 2008;51:31-43; Int J Cardiol. 2006;113:4-11
    Journal of Cardiac Failure
    2009;15:83-97
 9




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##### Table of Contents



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 40-50% New England Journal of Medicine,1999;341:1715-24. supra., p. 9]
  Challenges
    in Reimbursement
  FAMILION FAMILION FAMILION FAMILION in-network FAMILION FAMILION in-network FAMILION
  OTHER
    BUSINESS MATTERS
  Government
    Regulation
      FAMILION
   10




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Patents
    and Proprietary Technology
      
    One pending U.S patent application, four pending
    U.S. provisional patent applications, and one pending
    international patent application under the Patent Cooperation
    Treaty relating to genetic markers associated with response to
    antidepressants, namely vilazodone, composition of vilazodone
    and methods of use;
    One issued U.S. patent (expiry date of June 2024) and
    one pending U.S. patent application relating to Stedivaze
    formulation and process of preparation;
    Two pending U.S. provisional patents relating to LQTS;
    Two issued U.S. patents (expiry dates of May 2024
    (compound) and December 2025 (method of treatment)), three
    pending U.S. patent applications, three issued foreign
    patents in India, Mexico and New Zealand, forty-two pending
    foreign patent applications in Europe, Canada, Japan, Australia,
    and eighteen other countries, and one pending international
    patent application under the Patent Cooperation Treaty relating
    to substituted pyrimidine compounds and methods of use;
    Three pending U.S. patent applications, sixteen pending
    foreign patents in Europe, Canada, Japan, Australia and twelve
    other countries, one pending international patent application
    under the Patent Cooperation Treaty relating to ATL313;
    Two issued U.S. patents (expiry dates of November 2025
    (composition of matter) and May 2027 (process of
    manufacturing)), three pending U.S. patent applications,
    four issued foreign patents in Mexico, New Zealand, Russia and
    Singapore, thirty-two pending foreign patent applications in
    Europe, Canada, Japan, Australia and seventeen other countries
    relating to ATL844;
    Three pending U.S. patent applications and two pending
    international patent applications under the Patent Cooperation
    Treaty relating to ATL1222;
    One issued U.S. patent (expiry date of October 2027), one
    pending U.S. patent application, and thirteen pending
    foreign patent applications in Europe, Canada, Japan, Australia
    and nine other countries relating to ATL359;
    Five issued U.S. patents (expiry dates of April 2025 (A2A
    antagonists), April 2027 (pyridyl substituted xanthines and
    derivatives of 8-substituted xanthines), May 2027 (pyrazolyl
    substituted xanthines) and August 2027 (A2B antagonists)), five
    pending U.S. patent applications, two pending
    U.S. provisional patent applications, and nineteen pending
    foreign patent applications in Europe, Canada, Japan, Australia
    and eight other countries relating to our adenosine-related
    product pipeline;
    One pending U.S. patent application, thirteen pending
    foreign patent applications in Europe, Canada, Japan, Australia
    and nine other countries, and two pending international patent
    applications under the Patent Cooperation Treaty relating to
    beta catenin; 11




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
    Two pending U.S. patent applications and five pending
    foreign patent applications in Europe, Canada and Japan relating
    to PLK3;
    One pending U.S. patent application, one pending foreign
    patent application in Europe relating to compounds and methods
    for treating or preventing autoimmune diseases;
    Three issued U.S. patents (expiry dates of March 2022
    (colon cancer gene expression), July 2023 (pyrrole compounds for
    colon cancer) and February 2025 (compound centric signatures)),
    five pending U.S. patent applications and two pending
    foreign patent applications in Europe relating to cancer gene
    expression, therapeutic targets, AVN944 biomarkers, and
    identification of therapeutic agents;
    One pending U.S. patent application, twenty issued foreign
    patents in Europe, Canada, Mexico, India, Korea, Singapore and
    South Africa, and seven pending foreign patent applications in
    Europe, Canada and Japan relating to MDR-1;
    One issued U.S. patent (expiry date of May
    2020) relating to CYP3AX;
    One issued U.S. patent (expiry date of August 2021), and
    three pending foreign patent applications in Europe, Canada and
    Japan relating to CYP3A4 and CYP3A7;
    Two pending U.S. patent applications, eleven issued foreign
    patents in Europe, and two pending foreign patent applications
    in Canada and Japan relating to the CYP2D6;
    One pending U.S. patent application and nineteen issued
    foreign patents in Europe relating to CYP2B6;
    One pending U.S. patent application and one pending foreign
    patent application in Europe relating to CYP2C8;
    One pending U.S. patent application relating to MRP-1;
    One pending U.S. patent application and two pending foreign
    patent applications in Europe and Canada relating to TPMT;
    Three pending U.S. patent applications and one pending
    foreign patent application in Europe relating to OCT1;
    Eleven issued foreign patents in Europe relating to CYP3A5;
    One issued U.S. patent (expiry date of January 2021), nine
    issued foreign patents in Europe, and two pending foreign patent
    applications in Canada and Japan relating to hPXR;
    One issued U.S. patent (expiry date of May
    2021) relating to GSTT1;
    One issued U.S. patent (expiry date of December
    2024) relating to CDK5 genetic markers associated with
    galantamine response;
    One issued U.S. patent (expiry date of April
    2024) relating to methods of obtaining and using haplotype
    data;
    One issued U.S. patent (expiry date of August
    2018) relating to the method to evaluate the ability to
    metabolize pharmaceuticals and the compositions thereof; and
    One issued U.S. patent (expiry date of May
    2019) relating to UGT1.    
    Eleven issued U.S. patents (expiry dates of September 2014
    (composition of matter), April 2016 (intermediates), December
    2019 (process), January 2020 (intermediates), May 2020 (novel
    uses), November 2020 (intermediates), May 2021 (novel uses),
    September 2022 (second medical use) and September 2023
    (polymorphic forms)); three pending U.S. patent
    applications, three-hundred-thirty-nine issued foreign patents,
    fifty-four pending foreign patent applications and one pending
    international patent application under the Patent Cooperation
    Treaty owned by Merck relating to vilazodone, intermediates and
    polymorphic 12




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forms thereof, methods for manufacturing vilazodone, and methods
    of using vilazodone to treat depression, other anxiety disorders
    and other medical uses;  
    Four issued U.S. patents (expiry dates of June 2019), one
    pending U.S. patent application, seventy-two issued foreign
    patents, thirteen 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 Stedivaze compositions, methods of using
    Stedivaze for myocardial perfusion imaging and other imaging
    modalities and a unit dose;
    One issued U.S. patent (expiry date of May 2015) owned
    by the University of Massachusetts relating to a use for
    Stedivaze;
    One issued U.S. patent (expiry date of May
    2018) 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 U.S. patent application, one issued foreign
    patent, and two pending foreign patent applications owned by the
    National Institutes of Health relating to methods for treating
    cancer;
    Thirteen issued U.S. patents (expiry dates of July 2014
    (method for treating restenosis with A2A agonists and treating
    inflammatory response with A2A agonists), March 2016 (method for
    treating inflammatory diseases with A2A agonists), February 2018
    (use of A2B antagonists in treating respiratory diseases),
    February 2020 (A2B antagonists), January 2022 (treating
    inflammatory response), October 2022 (2-propynyl adenosine
    analogs having A2A agonist activity), July 2025 (allosteric
    enhancers of A1 adenosine receptors), March 2026 (agonist
    allosteric enhancers at human A1 adenosine receptors), May 2026
    (ATL313 and other A2A agonists), October 2026 (2-polycyclic
    propynyl adenosine analogs having A2A activity) and May 2027
    (ATL313 and other A2A agonists and 2-propynyl adenosine analogs
    having A2A agonist activity)), eleven pending U.S. patent
    applications, one pending U.S. provisional patent
    application, nine issued foreign patents, and fifteen pending
    foreign patent applications owned by the University of Virginia
    Patent Foundation relating to our substantial adenosine-related
    product pipeline;
    Five issued U.S. patents (expiry dates of October 2016
    (LQT1/KCNQ1), December 2016 (LQT1/KCNQ1), August 2017
    (LQT1/KCNQ1), July 2018 (LQT2/KCNH2) and August 2019
    (LQT2/KCNH2)), six issued foreign patents in Europe, Canada,
    Japan, Australia and one other country, and five pending foreign
    patent applications in Europe, Canada and Japan owned by the
    University of Utah relating to the diagnosis of inherited LQTS;
    Five issued U.S. patents (expiry dates of October 2016
    (LQT1/KCNQ1), December 2016 (LQT1/KCNQ1) and August 2017
    (LQT1/KCNQ1)), six issued foreign patents in Europe, Canada,
    Japan, Australia and one other country, and two pending foreign
    patent applications in Europe and Canada owned by Genzyme
    Corporation relating to the diagnosis of inherited LQTS;
    One pending U.S. patent application and three pending
    foreign patent applications in Europe, Canada and one other
    country and one pending international patent application under
    the Patent Cooperation Treaty owned by Newfound Genomics
    relating to the diagnosis of inherited ARVC;
    Three pending U.S. patent applications, sixteen issued
    foreign patents in Europe, Japan, Australia and two other
    countries, and four pending foreign patent applications in
    Europe, Canada and Japan owned by CHU Tours relating to the use
    of the FCGR3A V158F variant to predict certain phenotypes,
    including rituximab efficacy;
    One issued U.S. patent (expiry date of June
    2017) controlled by Innate Pharma relating to genotyping
    the FCGR3A V158F variant;
    One pending U.S. patent application owned by the University
    of Alabama-Birmingham relating to the use of certain FCGR2B
    variants to predict certain phenotypes; 13




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
    One issued U.S. patent (expiry date of August
    2015) 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 pending U.S. patent application owned by St. Jude
    Childrens Research Hospital (exclusively licensed to
    Specialty Laboratories, Inc.) relating to gamma glutamyl
    hydrolase activity;
    One issued U.S. patent (expiry date of June
    2012) owned by Yale University (exclusively sublicensed to
    Siemens Medical Solutions Diagnostics) relating to the coupled
    amplification and sequencing of DNA; and
    One issued U.S. patent (expiry date of October
    2020) owned by Vanderbilt University relating to a genetic
    marker predictive of drug-induced cardiac arrhythmia.  Backlog
    Employees
    Environmental
    Matters
    Significant
    Customers and Geographical Information
    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
  If we
    are unable to raise additional capital when needed in the
    future, we might be unable to execute our operating and
    development plans, and if we succeed in raising capital, we
    might dilute your percentage ownership of the common stock or
    might subject our company to fixed payment obligations and
    restrictive covenants.
   14




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
    partnering opportunities for the marketing of vilazodone;
    partnering opportunities for the development and marketing of
    Stedivaze;
    sales of non-core assets; and/or
    sales of equity and debt securities.      Given
    our current product development efforts, which have resulted in
    significant net losses, we expect to incur further net losses
    for the foreseeable future.
      If we
    are unable to obtain marketing approval of vilazodone, our
    results of operations will suffer.
     15




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We may
    not successfully develop or derive revenues from any
    products.
    
    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 safely manufactured in sufficient
    quantities at reasonable costs;
    obtain and maintain regulatory approvals for them; and
    market them successfully.    We
    have never marketed a drug before, and if we are unable to
    establish an effective sales force and marketing infrastructure
    either directly or in collaboration with a third party, we may
    not be able to commercialize our product candidates
    successfully.
    If
    physicians and patients do not accept and use our 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 safety and effectiveness of
    our drugs;
    adequate reimbursement for our products from payors; and
    effectiveness of marketing and distribution efforts by us and
    our licensees and distributors, if any.   16




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If our
    products are not granted adequate reimbursement from third-party
    payors, we may be unable to successfully commercialize them and
    we may never achieve widespread market acceptance of our
    products.
      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
  Because
    a significant portion of our total assets are represented by
    goodwill and indefinite-lived intangible assets that are subject
    to mandatory annual and potentially interim impairment
    evaluations and definite-lived intangible assets that are
    reviewed for impairment if certain conditions exist, we could be
    required to write-off some or all of this goodwill and
    intangible assets, which may adversely affect our financial
    condition and results of operations.
    We
    might enter into new acquisitions that are difficult to
    integrate, disrupt our business, dilute stockholder value or
    divert management attention.
    
    difficulties in integrating the operations, technologies,
    products and personnel 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; 17




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
    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;
    unexpected expenses resulting from the acquisition;
    potential unknown liabilities associated with acquired
    businesses;
    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 approved methods to produce these drugs
    using appropriate quality controls and at commercially viable
    rates.
    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.
  and/or
 18




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New
    drug development is a lengthy and complex process, and we may be
    unable to commercialize any of the products we
    develop.
    
    identify compounds with chemical, pharmacokinetic, and
    pharmacodynamic properties appropriate for human development;
    complete nonclinical studies related to the pharmacologic and
    toxicologic properties of the compound;
    submit an IND to the FDA or equivalent application to other
    regulatory agencies to begin
    first-in-human
    studies;
    undertake clinical trials to establish the efficacy, safety, and
    other aspects of our drug candidates;
    successfully manufacture drug substance and drug product for
    clinical trial and commercial uses;
    expend significant resources;
    maintain and expand our intellectual property rights;
    obtain, where necessary, marketing approvals from the FDA and
    other regulatory agencies for the intended indication; and
    find collaborative partners with manufacturing and commercial
    capabilities for our current and future drug candidates.    
    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 acquire sufficient resources to assist in
    conducting clinical trials; and
    the inability to establish the safety and efficacy or clinical
    utility of our products.    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.
    Covenants
    in our convertible notes restrict our financial and operational
    flexibility.
   19




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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;
    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.     20




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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.
    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.
   21




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Risk
    Factors Relating to Regulatory Matters
  Preclinical
    and clinical trials are time consuming, expensive, and uncertain
    processes.
      
    the size of the patient population;
    the proximity of patients to clinical sites;
    the eligibility criteria for the trial and the demands of
    completing the trial;
    alternative therapies or technologies; and
    competing clinical trials and new drugs approved for the
    conditions or indications we are investigating.        Regulatory
    approval of vilazodone or other products may be delayed, may
    require additional studies to be conducted or may not be
    obtained.
   22




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
    we must demonstrate through clinical trials that the proposed
    drug product is safe and effective for its intended use;
    data obtained from preclinical and clinical activities are
    susceptible to varying interpretations which could delay, limit
    or prevent regulatory approvals; and
    we have limited experience in manufacturing and supply of the
    drug substance and drug product, which is necessary to gain
    regulatory approval and to commercialize the drug product.  Even
    if our drug candidates obtain regulatory approval, we will be
    subject to on-going government regulation.
          Risks
    Related to Our Dependence on Third Parties
  We
    rely on third-party manufacturers and we or such third parties
    may encounter failures or difficulties that could delay the
    clinical development or regulatory approval of our drug
    candidates, or their ultimate commercial production if
    approved.
   23




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
    availability or contamination of raw materials and components
    used in the manufacturing process, particularly those for which
    we have no other source or supplier;
    capacity of our facilities or those of our contract
    manufacturers;
    facility contamination by microorganisms or viruses or cross
    contamination;
    compliance with regulatory requirements, including Form 483
    notices and Warning Letters;
    changes in forecasts of future demand;
    timing and actual number of production runs;
    production success rates and bulk drug yields; and
    timing and outcome of product quality testing.    We
    rely on third parties to conduct our clinical trials and many of
    our preclinical studies. If those parties do not successfully
    carry out their contractual duties or meet expected deadlines,
    our drug candidates may not advance in a timely manner or at
    all.
   24




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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
  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-sponsored entities in the development and marketing
    of products and services.
   25




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
    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.  In the
    U.S. there have been, and we expect there will continue to be, a
    number of federal and state proposals to reform the health care
    system in ways that could adversely impact the available
    reimbursement for, and therefore our ability to sell our
    products profitably.
   26




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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
  Conversion
    of outstanding convertible notes and exercise of outstanding
    warrants could significantly dilute the ownership interests of
    existing stockholders.
    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.
   27




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##### Table of Contents



Our
    directors, executive officers and their affiliated entities have
    substantial control over us and could limit the ability of other
    stockholders to influence the outcome of key transactions,
    including changes of control.
    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
    could be subject to class action litigation due to stock price
    volatility, which, if it occurs, will distract our management
    and could result in substantial costs or large judgments against
    us.
    Our
    corporate documents and Delaware Law make a takeover of our
    company more difficult, which could prevent certain changes in
    control and limit the market price of the common
    stock.
   28




---



##### Table of Contents



We
    currently do not intend to pay dividends on our common stock and
    consequently, investors only opportunity to achieve a
    return on their investment is if the price of our common stock
    appreciates.
    Future
    equity issuances or a sale of a substantial number of shares of
    our common stock may cause the price of our common stock to
    decline.
    ITEM 1B.
    UNRESOLVED
    STAFF COMMENTS    ITEM 2.
    PROPERTIES    Approximate




ExpirationLocation

Square Footage


Use

DateOne Gateway Center, Suite 702 
    Newton, Massachusetts


6,700


Corporate office


08/31/115 Science Park 
    New Haven, Connecticut


37,400


Office and laboratory


01/31/11310
    4th Street,

    NE 
    Charlottesville, Virginia


5,000


Office


04/30/111180 Seminole Trail, Route 29 North 
    Charlottesville, Virginia


6,400


Laboratory


07/31/111630-1670
    Discovery Drive 
    Charlottesville, Virginia


3,700


Laboratory


10/31/1094B Industrial Road 
    Troy, Virginia


1,000


Laboratory


05/31/109121 Anson Way, Suite 100 
    Raleigh, North Carolina


1,000


Office


Tenant-at-Will    29




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##### Table of Contents



ITEM 3.
    LEGAL
    PROCEEDINGS   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, 2010First Quarter

$
15.94


$
10.39Second Quarter

$
17.00


$
9.00Third Quarter

$
21.94


$
14.62Fourth Quarter

$
22.39


$
14.65Fiscal Year Ended March 31, 2009First Quarter

$
19.68


$
14.25Second Quarter

$
19.59


$
12.74Third Quarter

$
16.46


$
7.15Fourth Quarter

$
11.93


$
6.38   Holders
    of Common Stock
    Dividends
   30




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##### Table of Contents



Price
    Performance
    Comparison
    of 5 Year Cumulative Total Return
 Assumes Initial Investment of $100
 March 2010
  
  Company/NASDAQ Stock Market/NASDAQ Biotechnology
    Index


3/31/2005


3/31/2006


3/31/2007


3/31/2008


3/31/2009


3/31/2010CLINICAL DATA


$
100



$
125



$
127



$
170



$
99



$
178NASDAQ Stock Market (US and Foreign securities)


$
100



$
118



$
123



$
117



$
63



$
100NASDAQ Biotechnology Index


$
100



$
129



$
119



$
120



$
105



$
145   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, 2008Avalon Pharmaceuticals, Inc.

May 28, 2009    31




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##### Table of Contents



Years Ended March 31,2010


2009


2008


2007


2006(In thousands, except per share amounts)Consolidated Statements of Operations DataRevenues

$
13,085


$
10,442


$
5,107


$
3,828


$
1,660Cost of revenues


6,244



6,489



2,627



2,240



3,045Gross profit


6,841



3,953



2,480



1,588



(1,385
)OPERATING EXPENSES:Research and development


56,785



44,134



16,889



9,265



2,797Sales and marketing


8,155



7,764



3,612



1,210



408General and administrative


23,699



19,730



16,806



14,959



6,919Restructuring and lease exiting costs


2,447















Purchased in-process research and development






55,100











36,300Transaction costs incurred in connection with the Avalon
    acquisition


1,978















Total operating expenses


93,064



126,728



37,307



25,434



46,424Operating loss


(86,223
)


(122,775
)


(34,827
)


(23,846
)


(47,809
)Interest expense


(9,128
)


(1,802
)


(76
)


(220
)


(228
)Interest income


80



716



2,020



323



61Other income (expense), net


1,771



179



305



210



(59
)Loss from continuing operations before taxes


(93,500
)


(123,682
)


(32,578
)


(23,533
)


(48,035
)Benefit from (provision for) income taxes










230



(233
)


(102
)Loss from continuing operations


(93,500
)


(123,682
)


(32,348
)


(23,766
)


(48,137
)Income (loss) from discontinued operations, net of taxes


4,987



(8,756
)


(2,982
)


(13,756
)


(2,744
)Net loss


(88,513
)


(132,438
)


(35,330
)


(37,522
)


(50,881
)Preferred stock dividend














(104
)


(97
)Net loss applicable to common stockholders

$
(88,513
)

$
(132,438
)

$
(35,330
)

$
(37,626
)

$
(50,978
)(Loss) income per basic and diluted share:Continuing operations

$
(3.77
)

$
(5.63
)

$
(1.69
)

$
(1.68
)

$
(5.39
)Discontinued operations


0.20



(0.40
)


(0.16
)


(0.97
)


(0.30
)Net loss

$
(3.57
)

$
(6.03
)

$
(1.85
)

$
(2.65
)

$
(5.69
)Cash dividends paid per common share

$



$



$



$



$
0.04Weighted average shares:Basic and diluted


24,769



21,962



19,081



14,186



8,953   As of March 31,2010


2009


2008


2007


2006(In thousands)Consolidated Balance Sheet Data:Cash, cash equivalents and marketable securities

$
49,245


$
56,355


$
67,480


$
14,071


$
7,225Total assets


98,955



120,197



129,448



87,490



109,789Long-term obligations


57,674



63,123



5,122



3,236



7,345Stockholders equity


3,893



29,412



106,075



50,720



59,789  32




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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
    including vilazodone;
    our ability to successfully design and conduct our planned
    clinical trials for Stedivaze and other potential products;
    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 U.S. 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
  1A 2A best-in-class
   33




---



##### Table of Contents



Therapeutics:
  Vilazodone
  1A Current Therapeutic Research
     34




---



##### Table of Contents



Stedivaze
  2A
  best-in-class
  . Journal of Nuclear Cardiology,
  Other
    Therapeutic Products
  2A 2A
  and/or 2B
  2A
   35




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##### Table of Contents



Genetic
    Tests
  FAMILION
  FAMILION
  FAMILION FAMILION FAMILION FAMILION in-network FAMILION FAMILION in-network FAMILION
  Financial
    Operations Overview
  Revenue.
  Cost of Revenue.
  Sales and Marketing Expense.
  Research and Development Expense.
  General and Administrative Expense.
  Interest and Other Income (Expense),
    Net.
 36




---



##### Table of Contents



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 
   37




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##### Table of Contents



Income Taxes 
  Recent
    Accounting Pronouncements
  EITF 08-1, Revenue Arrangements with Multiple Deliverables No. 2009-13. No. 2009-13 No. 2009-13 No. 2009-13
  Results
    of Operations
  Fiscal
    Year Ended March 31, 2010 Compared to Fiscal Year Ended
    March 31, 2009
  Revenue.
  Gross Profit.
 38




---



##### Table of Contents



Research and Development Expense.
  Sales and Marketing Expense.
  General and Administrative Expense.
 39




---



##### Table of Contents



Restructuring and Lease Exiting Costs.
  Purchased In-Process Research and Development
    Expense.
  Transaction Costs Incurred in Connection with the Avalon
    Acquisition.
  Interest and Other Income (Expense),
    Net.
  Fiscal
    Year Ended March 31, 2009 Compared to Fiscal Year Ended
    March 31, 2008
  Revenue.
  Gross Profit.
 40




---



##### Table of Contents



Research and Development Expense.
  Sales and Marketing Expense.
  General and Administrative Expense.
  Purchased In-Process Research and Development
    Expense.
 41




---



##### Table of Contents



Interest and Other Income (Expense),
    Net.
  Liquidity
    and Capital Resources
    Years Ended March 31,2010


2009


2008(In thousands)Cash (used in) provided by continuing operations:Operating activities

$
(63,698
)

$
(56,589
)

$
(18,491
)Investing activities


5,747



(6,041
)


(25,649
)Financing activities


39,658



71,470



75,267Cash provided by (used in) discontinued operations


12,358



(6,279
)


9,135Effect of exchange rate






(2,136
)


422(Decrease) increase in cash and cash equivalents

$
(5,935
)

$
425


$
40,684       Payments
    Due by Period
  Fiscal 2012


Fiscal 2014through


through


AfterTotal


Fiscal 2011


Fiscal 2013


Fiscal 2015


Fiscal 2015(In thousands)Contractual Obligations:Short and long-term
    debt(1)

$
103,851


$
12,450


$
19,712


$
11,969


$
59,720Capital lease
    obligations(1)


323



156



167







Operating lease obligations


1,182



948



221



13



Total contractual cash obligations

$
105,356


$
13,554


$
20,100


$
11,982


$
59,720     (1)

    
    Includes interest expense       42




---



##### Table of Contents



Off-Balance
    Sheet Arrangements
    ITEM 7A.
    QUANTITATIVE
    AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK    Interest
    Rate Risk
    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 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)
 43




---



##### Table of Contents



Internal Control  Integrated
    Framework
    Changes
    in Internal Controls
  Rules 13a-15(f) 15d-15(f)
 44




---



##### Table of Contents



REPORT OF
    INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
      Internal Control  Integrated Framework
        Internal Control  Integrated Framework
    
    45




---



##### 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
    ACCOUNTING FEES AND SERVICES   PART IV  ITEM 15.
    EXHIBITS,
    FINANCIAL STATEMENT SCHEDULES  Consolidated Financial Statements
    Consolidated Financial Statement
    Schedules
    Exhibits
  Form 10-K.
 46




---



##### Table of Contents



SIGNATURES      
        
          
       
       
      47




---



##### Table of Contents



48




---



##### Table of Contents



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,
    2010 and 2009


F-3Consolidated Statements of Operations for the
    Years Ended March 31, 2010, 2009 and 2008


F-4Consolidated Statements of Stockholders
    Equity for the Years Ended March 31, 2010, 2009 and 2008


F-5Consolidated Statements of Cash Flows for the
    Years Ended March 31, 2010, 2009 and 2008


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 31,2010


2009(In thousands, except share and per share amounts)ASSETSCurrent Assets:Cash and cash equivalents

$
49,245


$
55,180Marketable securities, at fair value






1,175Accounts receivable, net


2,851



2,471Prepaid expenses and other current assets


1,488



1,240Assets of discontinued operations






18,541Total current assets


53,584



78,607Property, plant and equipment, net


2,795



2,942Goodwill


31,849



29,496Intangible assets, net


10,665



4,747Other assets, net


62



4,405TOTAL ASSETS

$
98,955


$
120,197LIABILITIES AND STOCKHOLDERS EQUITYCurrent Liabilities:Current portion of long-term debt

$
6,635


$
6,337Current portion of capital leases


138



730Accounts payable


5,550



5,562Accrued expenses


25,065



6,131Liabilities of discontinued operations






8,902Total current liabilities


37,388



27,662Long-Term Liabilities:Long-term debt, net of current portion


11,329



17,964Convertible note payable (related-party), net of unamortized
    discount


30,129



28,868Capital lease obligations, net of current portion


157



226Other long-term liabilities


20



26Contingent acquisition costs (Note 4)


16,039



16,039Total long-term liabilities


57,674



63,123Commitments and contingencies (Note 9)Stockholders Equity:Preferred Stock, $.01 par value, 1,500,000 shares
    authorized; none issued and outstanding






Common stock, $.01 par value, 60,000,000 shares
    authorized; 26,519,000 and 22,742,000 shares issued and
    outstanding at March 31, 2010 and 2009, respectively


265



227Additional paid-in capital


343,345



276,788Accumulated deficit


(339,717
)


(251,204
)Accumulated other comprehensive income






3,601Total stockholders equity


3,893



29,412TOTAL LIABILITIES AND STOCKHOLDERS EQUITY

$
98,955


$
120,197    F-3




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    STATEMENTS OF OPERATIONS  Years Ended March 31,2010


2009


2008(In thousands, except share and pershare amounts)Revenues

$
13,085


$
10,442


$
5,107Cost of revenues


6,244



6,489



2,627Gross profit


6,841



3,953



2,480OPERATING EXPENSES:Research and development


56,785



44,134



16,889Sales and marketing


8,155



7,764



3,612General and administrative


23,699



19,730



16,806Restructuring and lease exiting costs


2,447







Purchased in-process research and development






55,100



Transaction costs incurred in connection with the Avalon
    acquisition


1,978







Total operating expenses


93,064



126,728



37,307Operating loss


(86,223
)


(122,775
)


(34,827
)Interest expense


(1,367
)


(1,257
)


(76
)Interest expense (related-party)


(7,761
)


(545
)


Interest income


80



716



2,020Other income, net


1,771



179



305Loss from continuing operations before taxes


(93,500
)


(123,682
)


(32,578
)Benefit from income taxes










230Loss from continuing operations


(93,500
)


(123,682
)


(32,348
)Income (loss) from discontinued operations, net of taxes


4,987



(8,756
)


(2,982
)Net loss

$
(88,513
)

$
(132,438
)

$
(35,330
)(Loss) income per basic and diluted share:Continuing operations

$
(3.77
)

$
(5.63
)

$
(1.69
)Discontinued operations


0.20



(0.40
)


(0.16
)Net loss

$
(3.57
)

$
(6.03
)

$
(1.85
)Weighted average shares:Basic and diluted


24,769



21,962



19,081     F-4




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIESCONSOLIDATED STATEMENTS OF STOCKHOLDERS
    EQUITY
    FOR THE YEARS ENDED MARCH 31, 2010, 2009 AND 2008
    (In thousands)  Common











AccumulatedPreferred


Preferred


Common


Stock


Additional








OtherStock


Stock Par


Stock


Par


Paid-in


Accumulated


Treasury


Comprehensive





ComprehensiveShares


Value


Shares


Value


Capital


Deficit


Stock


Income


Total


Loss(In thousands)BALANCE at April 1, 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 $4,536










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 to a
    related party


















10,767















10,767Beneficial conversion feature of the convertible notes with a
    related party


















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



29,412Equity issued in connection with the Avalon acquisition










801



8



11,556















11,564Public offering, net of transaction costs of $3,262










2,750



28



44,148















44,176Exercise of stock options, net of shares surrendered










149



1



1,649















1,650Exercise of stock warrants










41



1



899















900Stock-based compensation










36







8,305















8,305Translation adjustment






























(2,279
)


(2,279
)

$
(2,279
)Change in unrealized gain on marketable securities






























(1,322
)


(1,322
)


(1,322
)Net loss






















(88,513
)










(88,513
)


(88,513
)Total comprehensive loss





































$
(92,114
)BALANCE at March 31, 2010





$




26,519


$
265


$
343,345


$
(339,717
)

$



$



$
3,893    F-5




---



##### Table of Contents





CLINICAL
    DATA, INC. AND SUBSIDIARIES



CONSOLIDATED
    STATEMENTS OF CASH FLOWS  Years Ended March 31,2010


2009


2008(In thousands)CASH FLOWS FROM OPERATING ACTIVITIES:Net loss

$
(88,513
)

$
(132,438
)

$
(35,330
)(Income) loss from discontinued operations


(4,987
)


8,756



2,982Loss from continuing operations


(93,500
)


(123,682
)


(32,348
)Adjustments to reconcile loss from continuing operations to net
    cash used in operating activities:Depreciation and amortization


2,949



1,670



673Stock-based compensation


8,305



8,130



5,904Non-cash milestones paid (or payable) to Merck under license
    agreement


15,718







3,619Provision for doubtful accounts


1,749



1,015



189Purchased in-process research and development






55,100



Accretion of discount on convertible note with related party


1,261



106



Gain on Avalon stock held by Clinical Data prior to the merger


(1,773
)






Non-cash restructuring and lease exiting costs


1,783







Loss on sales of equipment






51



10Changes in current assets and liabilities, net of acquired
    assets and liabilities:Accounts receivable


(2,087
)


(2,243
)


(512
)Prepaid expenses and other current assets


81



(553
)


(319
)Other assets


1,784



155



(229
)Accounts payable and other liabilities


32



3,662



4,522Cash used in continuing operations


(63,698
)


(56,589
)


(18,491
)Cash used in discontinued operations


(885
)


(3,661
)


(6,041
)Net cash used in operating activities


(64,583
)


(60,250
)


(24,532
)CASH FLOWS FROM INVESTING ACTIVITIES:Purchases of equipment


(859
)


(1,241
)


(511
)Purchases of marketable securities










(15,275
)Proceeds from sales of equipment, net of transaction costs


1,244







84Proceeds from sales of marketable securities


1,175



12,050



2,050Cash provided by (used in) business combinations, net of cash
    acquired


4,187



(16,850
)


(11,997
)Cash provided by (used in) investing activities 
    continuing operations


5,747



(6,041
)


(25,649
)Cash provided by (used in) investing activities 
    discontinued operations


13,243



(1,033
)


20,459Net cash provided by (used in) investing activities


18,990



(7,074
)


(5,190
)      F-6




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  Years Ended March 31,2010


2009


2008(In thousands)CASH FLOWS FROM FINANCING ACTIVITIES:Borrowings under other debt arrangements






50,000



Payment on debt and capital leases


(7,068
)


(3,703
)


(413
)Proceeds from the sale of common stock and warrants, net of
    transaction costs


44,176



24,964



71,364Exercise of stock options and warrants


2,550



209



4,316Cash provided by financing activities  continuing
    operations


39,658



71,470



75,267Cash used in financing activities  discontinued
    operations






(1,585
)


(5,283
)Net cash provided by financing activities


39,658



69,885



69,984EFFECT OF EXCHANGE RATE CHANGES ON CASH AND CASH EQUIVALENTS






(2,136
)


422NET (DECREASE) INCREASE IN CASH AND CASH EQUIVALENTS


(5,935
)


425



40,684CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD


55,180



54,755



14,071CASH AND CASH EQUIVALENTS, END OF PERIOD

$
49,245


$
55,180


$
54,755Supplemental disclosure of cash flow information:Cash paid during the year for:Interest

$
9,208


$
930


$
76Income taxes

$



$



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

$
68


$
307


$
567Equity issued in business acquisitions

$
11,564


$



$
Accrued acquisition costs

$



$
207


$
Debt issued in business acquisitions

$



$
25,200


$
Equity issued to acquire technology rights

$



$



$
3,619Issuance of common stock upon note conversion

$



$



$
2,337      F-7




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
 NOTES TO
    CONSOLIDATED FINANCIAL STATEMENTS



FOR THE
    YEARS ENDED MARCH 31, 2010, 2009 AND 2008  (1)
    Nature of
    Business and Basis of Presentation  Nature
    of Business
    2A best-in-class
  first-in-human 2A B-cell
      Basis
    of Presentation
       F-8




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      
    partnering opportunities for the marketing of vilazodone;
    partnering opportunities for the development and marketing of
    Stedivaze;
    license, sublicense, or other relationships with third parties
    relating to the development programs of its preclinical
    compounds
    and/or
    patents;
    sale of non-core assets; and/or
    sale of equity or debt securities.    (2)
    Significant
    Accounting Policies  Principles
    of Consolidation
    Use
    of Estimates
    Cash
    and Cash Equivalents
   F-9




---



##### Table of Contents



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


2009


2008(In thousands)Allowance for uncollectible accounts  beginning of
    year

$
1,292


$
500


$
346Provisions


1,749



1,015



189Less: deductions


(518
)


(223
)


(35
)Allowance for uncollectible accounts  end of year

$
2,523


$
1,292


$
500   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
       F-10




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Revenue
    Recognition
      Research
    and Development Costs
    Income
    Taxes
      Comprehensive
    Income (Loss)
   F-11




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    March 31,2010


2009(In thousands)Foreign currency translation adjustment

$



$
2,279Unrealized gain on investment in Avalon






1,322Total

$



$
3,601     Loss
    per Share
      2010


2009


2008(In thousands)Common stock options


3,911



3,630



2,539Common stock warrants


4,262



4,567



1,011Convertible note payable


6,111



6,111



Contingent value rights


41







Total


14,325



14,308



3,550   Equity-Based
    Compensation
    Concentration
    of Credit Risk
   F-12




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Fair
    Value of Financial Instruments
        Description

Level 1

Level 2

Level 3

Total(In thousands)Assets:Cash equivalents

$
38,193


$



$



$
38,193     Description

Level 1

Level 2

Level 3

Total(In thousands)Assets:Cash equivalents

$
37,659


$



$



$
37,659Marketable securities  Auction rate preferred
    securities










1,175



1,175Marketable securities  Avalon common stock


1,560











1,560     Auction RateSecurities(In thousands)Balance at March 31, 2009

$
1,175Auction rate preferred securities redeemed at par


(1,175
)Balance at March 31, 2010

$
   Segment
    and Geographical Information
     F-13




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Recent
    Accounting Pronouncements
  EITF 08-1, Revenue Arrangements with Multiple Deliverables No. 2009-13. No. 2009-13 No. 2009-13 No. 2009-13
  (3)
    Discontinued
    Operations    Vital
    Scientific
      Electa
    Lab
    Cogenics
   F-14




---



##### Table of Contents



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


2009


2008(In thousands)Revenue

$
499


$
27,018


$
50,381Loss from Operations Before Disposal:Loss before taxes

$
(485
)

$
(8,288
)

$
(9,518
)Income taxes


(14
)


(216
)


(1,365
)Loss from discontinued operations, net of taxes


(499
)


(8,504
)


(10,883
)Disposal:Gain/(loss) on disposal, net of taxes


5,486



(252
)


7,901Gain/(loss) from discontinued operations, net of tax

$
4,987


$
(8,756
)

$
(2,982
)   (4)
    Business
    Combinations  Adenosine
    Therapeutics, LLC
  32-month
       F-15




---



##### Table of Contents



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

$
10,699Debt


25,200Contingent acquisition costs


16,039Transaction costs


400$
52,338   (In thousands)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     2A best-in-class
       F-16




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Avalon
    Pharmaceuticals, Inc.
        (In thousands)Clinical Data common stock issued

$
9,602Contingent value rights


1,961Acquisition date fair value of Avalon common stock held by
    Clinical Data


2,010Cash paid in October 2008 for license to Avalon technology


1,000$
14,573   F-17




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (In thousands)Purchase Price AllocationCash and cash equivalents

$
4,187Prepaid expenses and other current assests


419Property and equipment


3,292Purchased in-process research and development costs


3,200Intangible asset  Completed technology (5 years)


3,700Intangible asset  Tradename (5 years)


600Goodwill


2,353Accounts payable


(1,851
)Accrued expenses and other current liabilities


(1,327
)Total purchase price

$
14,573               Business
    Combinations Business Combinations
 F-18




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Restructuring
    of Avalon Operations
         F-19




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (5)
    Property,
    Plant and Equipment    2010


2009(In thousands)Laboratory equipment

$
1,511


$
1,197Leasehold improvements


1,625



1,527Computer equipment and software


2,460



2,022Furniture and fixtures


292



1875,888



4,933Less: accumulated depreciation and amortization


(3,093
)


(1,991
)$
2,795


$
2,942     (6)
    Intangible
    Assets    AverageUsefulLife

2010


2009(In thousands)Completed technology

6.7 years

$
9,655


$
5,955In-process technology

N/A


3,200



Customer relationships

5.0 years


400



400Other

5.3 years


700



10013,955



6,455Less: accumulated amortization




(3,290
)


(1,708
)Intangible assets, net



$
10,665


$
4,747      F-20




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (7)
    Accrued
    Expenses    2010


2009(In thousands)Payroll and payroll-related expenses

$
4,679


$
2,020External research and development expenses


992



1,147Commissions, royalties and license fees


1,121



1,063Milestone payable to Merck


15,718



Other


2,555



1,901$
25,065


$
6,131   (8)
    Debt    2010


2009(In thousands)Notes payable, bearing interest at 6.5%, with monthly principal
    payments due through June 2011 and secured by certain of
    PGxHealths leasehold improvements

$
1,264


$
2,001Note 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


1,300



2,500Note payable, bearing interest at 6% with quarterly principal
    payments of $1,100 through July 13, 2013, secured by
    substantially all of the assets of the Company


15,400



19,800Convertible notes payable (related party), maturing
    February 25, 2017


50,000



50,00067,964



74,301Less: current portion


(6,635
)


(6,337
)unamortized discount


(19,871
)


(21,132
)$
41,458


$
46,832      F-21




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      2011

$
6,6352012


4,7292013


4,4002014


2,2002015


After


50,000Total

$
67,964   (9)
    Commitments
    and Contingencies  Litigation
    Contractual
    Commitments and Commercial Obligations
    Operating


CapitalYear Ending March 31,

Leases


Leases2011

$
948


$
1562012


190



1252013


31



422014


13



Thereafter






Total

$
1,182



323Less: amount representing interest






(28
)Total principal obligations






295Less: current portion






(138
)Long-term capital lease





$
157      F-22




---



##### 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
  Avalon
    Acquisition Commitments
   F-23




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    (10)
    Equity  Preferred
    Stock
    Common
    Stock
        3-for-2
           F-24




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
              (11)
    Income
    Taxes      2010


2009


2008(In thousands)Beginning uncertain tax benefits

$



$



$
Current year  increases


640







Current year  decreases










Settlements










Expire statutes










Ending uncertain tax benefits

$
640


$



$
  F-25




---



##### Table of Contents



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

Tax YearsUnited States


2007-2010United Kingdom


2007-2009     2010


2009


2008(In thousands)United States

$
(82,208
)

$
(124,410
)

$
(31,272
)Foreign


(11,292
)


728



(1,306
)$
(93,500
)

$
(123,682
)

$
(32,578
)     2010


2009


2008(In thousands)Current:Federal

$



$



$
(16
)Foreign










(214
)Total Current










(230
)Deferred:Federal










Foreign










Change in valuation allowance










Total Deferred










$



$



$
(230
)     2010


2009


2008(In thousands)Benefits from taxes at statutory rate

$
(31,790
)

$
(42,052
)

$
(11,076
)Stock-based compensation


2,243



2,606



1,072Change in valuation reserves


54,921



36,228



9,575Other


(25,374
)


3,218



199$



$



$
(230
)    F-26




---



##### Table of Contents



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


2009(In thousands)Deferred tax assets:Net operating losses

$
124,007


$
81,695Capitalized research costs


12,013



6,730Purchased intangibles


16,449



17,766Capital losses


5,977



4,545Tax credits


3,605



2,752Technology license fee


5,737



Other reserves and accrued liabilities


2,640



2,019Net deferred tax asset


170,428



115,507Less: valuation allowance


(170,428
)


(115,507
)$



$
       (12)
    Stock
    Incentive Plans and Equity Based Compensation       F-27




---



##### Table of Contents



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


AverageAverage


Remaining


AggregateNumber of


Exercise


Contractual


IntrinsicShares


Price


Term


Value(In thousands, except for per share amounts)Outstanding April 1, 2009


3,630


$
13.61Granted


925



16.42Cancelled/Expired


(491
)


15.20Exercised


(153
)


11.23Outstanding March 31, 2010


3,911


$
14.17



7.7 years


$
21,712Exercisable March 31, 2010


2,144


$
13.57



6.8 years


$
13,619Exercisable March 31, 2009


1,625


$
13.56Available for future grants March 31, 2010


444         2010


2009


2008(In thousands)Cost of revenues

$
253


$
258


$
301Sales and marketing


1,043



1,071



564Research and development


2,431



1,298



523General and administrative


4,578



5,503



4,516Stock based compensation expense, net

$
8,305


$
8,130


$
5,904        F-28




---



##### Table of Contents



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

2009

2008Weighted-average interest rate

1.25 - 2.63%

1.50 - 3.50%

2.75 - 4.75%Expected dividend yield

0.00%

0.00%

0.00%Expected lives

6 years

6 years

6 yearsExpected volatility

57 - 66%

65 - 69%

71 - 79%Weighted average grant date fair value

$9.64

$7.96

$12.30   (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, 20101st Quarter


2nd Quarter


3rd Quarter


4th
    Quarter(2)(In thousands, except per share amounts)Net revenue

$
3,695


$
3,042


$
3,128


$
3,220Gross profit


2,026



1,433



1,650



1,732Operating loss


(18,710
)


(16,643
)


(14,330
)


(36,540
)Loss from continuing operations


(20,246
)


(18,662
)


(16,184
)


(38,408
)Income from discontinued operations


4,837







150



Net loss


(15,409
)


(18,662
)


(16,034
)


(38,408
)Net (loss) income per basic and diluted share:Continuing operations

$
(0.88
)

$
(0.79
)

$
(0.63
)

$
(1.44
)Discontinued operations

$
0.21


$



$



$
   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



1,569Operating loss


(12,806
)


(67,438
)


(22,203
)


(20,328
)Loss from continuing operations


(12,526
)


(67,276
)


(22,403
)


(21,477
)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
)     (1)

    
    The operating loss for the quarter ended September 30, 2008
    includes $52.1 million related to in-process research and
    development expense arising from the acquisition of Adenosine
    Therapeutics.(2)

    
    The operating loss for the quarter ended March 31, 2010
    includes $15.7 million of research and development expense
    arising from the milestone payment due to Merck as a result of
    filing the NDA for vilazodone with the FDA. F-30




---



##### Table of Contents



EXHIBIT INDEX
  ExhibitNumber

Description1
.1

Purchase Agreement, dated October 28, 2009, among Clinical
    Data, Inc., Piper Jaffray & Co., Wedbush Morgan
    Securities, Inc., BMO Capital Markets Corp. and Roth Capital
    Partners LLC. Filed as Exhibit 1.1 to the Companys
    Current Report on
    Form 8-K
    filed with the Commission on October 28, 2009, and
    incorporated herein by reference.2
.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.2
.7

Stock Purchase Agreement, dated August 31, 2009, by and
    among Clinical Data, Inc., Avalon Pharmaceuticals, Inc.,
    PGxHealth, LLC and Intextron Corporation. Filed as
    exhibit 2.1 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 4, 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 as Exhibit 4.2 to the Companys
    Annual Report on
    Form 10-K,
    as filed with the Commission on June 15, 2009, and
    incorporated herein by reference.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.




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##### Table of Contents



ExhibitNumber

Description10
.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*

Amended and Restated Executive Employment Agreement of Andrew J.
    Fromkin effective as of September 14, 2009. Filed as
    Exhibit 99.1 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 18, 2009, and
    incorporated herein by reference.10
.7*

Amended and Restated Executive Employment Agreement of Caesar J.
    Belbel effective as of September 14, 2009. Filed as
    Exhibit 99.2 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 18, 2009, and
    incorporated herein by reference.10
.8*

Amended and Restated Executive Employment Agreement of C. Evan
    Ballantyne effective as of September 14, 2009. Filed as
    Exhibit 99.3 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 18, 2009, 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 September 14, 2009. Filed
    as Exhibit 99.4 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 18, 2009, 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

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
.18

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
.19

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
.20

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
.21

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.




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##### Table of Contents



ExhibitNumber

Description10
.22

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
.23

Contingent Value Rights Agreement, dated May 28, 2009,
    among Clinical Data, Inc. and American 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
.24

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
.25

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
.26

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
.27

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
.28

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
.29

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
.30

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
.31

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.10
.32

Amended and Restated UVAPF License Agreement, dated as of
    June 4, 2010 to be effective April 22, 1999, by and
    between the University of Virginia Patent Foundation and
    PGxHealth, LLC, as successor in interest to Adenosine
    Therapeutics, LLC. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on June 7, 2010, 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 has been granted with respect to portions
    of this exhibit. A complete copy of the agreement, including the
    redacted terms, has been separately filed with the Commission.
    
    Confidential treatment has been requested with respect to
    portions of this exhibit. A complete copy of the agreement,
    including redacted terms, has been separately filed with the
    Commission.