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UNITED STATES SECURITIES AND
    EXCHANGE COMMISSIONWashington, 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, 2007ORo

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-K Form 10-K Form 10-K.  YES þ o
  Rule 12b-2
  o o þ
  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, 2007
  PagePART
    1ITEM 1.

Business


1ITEM 1A.

Risk
    Factors


30ITEM 1B.

Unresolved Staff Comments


45ITEM 2.

Properties


45ITEM 3.

Legal
    Proceedings


45ITEM 4.

Submission of
    Matters to a Vote of Security Holders


46PART IIITEM 5.

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


46ITEM 6.

Selected
    Consolidated Financial Data


48ITEM 7.

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


49ITEM 7A.

Quantitative and
    Qualitative Disclosures about Market Risk


60ITEM 8.

Financial
    Statements and Supplementary Data


61ITEM 9.

Changes in and
    Disagreements with Accountants on Accounting and Financial
    Disclosure


61ITEM 9A.

Controls and
    Procedures


61ITEM 9B.

Other
    Information


62PART IIIITEM 10.

Directors,
    Executive Officers, and Corporate Governance


63ITEM 11.

Executive
    Compensation


66ITEM 12.

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


76ITEM 13.

Certain
    Relationships and Related Transactions, and Director
    Independence


78ITEM 14.

Principal
    Accounting Fees and Services


79PART IVITEM 15.

Exhibits and
    Financial Statement Schedules


80SIGNATURES


81Ex-21.1 Subsidiaries of the CompanyEx-23.1 Consent of Deloitte & Touche LLPEx-31.1 Section 302 Certification of the C.E.O.Ex-31.2 Section 302 Certification of the C.F.O.Ex-32.1 Section 906 Certification of the C.E.O. and C.F.O.




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NOTE REGARDING
    FORWARD-LOOKING STATEMENTS
  Form 10-K Form 10-K. Form 10-K Form 10-K.
 PART I  ITEM 1.
    BUSINESS  General
    TM
  TM
 1




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in vitro
  Company
    History
    TM TM
      and/or
   2




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OUR
    INDUSTRIES:
  Diagnostic
    and Genetic Testing Industries
  Sub-optimal
    trial-and-error g
     3




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FAMILION ® TM
    
    demonstrating pharmacogenetic and medical economic data to
    support test adoption and reimbursement;
    antiquated reimbursement formulas that do not adequately reflect
    the value of pharmacogenomic tests and the level of R&D and
    licensing costs required to bring tests to market;
    education for providers on how and when to incorporate
    pharmacogenetic testing into their delivery of care;
    the availability of validated pharmacogenetic associations
    producing tests with appropriate sensitivity and specificity for
    the specific clinical utility;
    the complexity of the genetic underpinnings of disease and drug
    response;
    other parties who have opposing interests in seeing these tests
    commercialized;
    uncertainty about the predictive value of genetic tests to
    accurately identify patients; and
    ethical, legal, regulatory, and social considerations. 4




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Development
    and Marketing of Drugs
  Journal of Health Economics
      and/or
 5




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Research Action
  
    Incidence rates of ADEs vary from 2 per 100 admissions to
    7 per 100 admissions among the hospitals that have
    conducted ADE studies;
    Patients who experienced ADEs were hospitalized an average of 8
    to 12 days longer than patients who did not suffer ADEs,
    and their hospitalization cost $16,000 to $24,000 more;
    Over 770,000 people are injured or die each year in
    hospitals from ADEs;
    National hospital expenses to treat patients who suffer ADEs
    during hospitalization are estimated at between $1.56 and
    $5.6 billion annually; and
    Studies indicate that anywhere from 28 to 95 percent of
    ADEs can be prevented.  Journal of the American Medical Association (JAMA) 2270-2279,
   6




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Lancet. 1545-53. JAMA 1998;279(23):1903-1907) American Journal of Psychiatry. http://www.fda.gov/cder/genomics/genomic_biomarkers_table.htm).
  Fee-for-service
    Pharmacogenomics and Molecular Biology Services
  http://www.phortech.com/2005seq.htm).
  st
  Genetic
    Engineering and Biotechnology News: BioMarket Trends: 20-22%
 7




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10-20% Bio Economic Research Associates
    
    researchers in academia and government laboratories answering
    basic science questions about gene structure and expression in
    plant, animal and lower species;
    drug discovery departments in pharmaceutical and biotechnology
    companies doing pathway analyses using gene expression tools to
    find new drug targets or biomarkers;
    academic and applied industrial researchers performing
    biodistribution studies of recombinant vaccine and gene therapy
    candidates;
    applied clinical departments in pharmaceutical and biotechnology
    companies exploring the role of genetic variation among human
    clinical trial patients in genotyping studies as it relates to
    selective sensitivity to, or metabolism of, drug candidates and
    issues in personalized medicine;
    quality control and related process development and
    manufacturing departments in biopharmaceutical firms seeking to
    adhere to current Good Manufacturing Practices (cGMP) regarding
    DNA sequence identity, DNA copy number, residual DNA and other
    requirements of the Chemistry, Manufacturing and Controls
    (CMC) sections in Investigational New Drug (IND) or New
    Drug Applications (NDA) and in post-launch cGMP manufacturing;
    customers or marketers of tests for genotypic markers of family
    inheritance patterns and other related tests such as disease
    susceptibility in animals (e.g., scrapie disease susceptibility
    in sheep); and
    molecular biology reagent, instrument and research tools
    companies requiring molecular biology services for quality
    control, component or other OEM contribution to their businesses.        
    provide a complete and comprehensive portfolio of services that
    spans the customers total requirements; 8




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
    offer the best and most reliable cutting edge technology service
    platforms commercially available;
    meet or exceed the customers turnaround time needs;
    generate the highest quality data and value-added analyses;
    provide an aggressive and competitive price that follows the
    technology maturation curve; and
    offer reliable, convenient , user-friendly customer-centric
    services.    In
    Vitro Diagnostic (IVD) Testing
          OUR
    COMPANIES
  PGxHEALTH
  Our
    Strategy
  and/or
  Developing
    and Commercializing Genetic Tests
   9




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FAMILION PGxPredict TM PGxPredict TM PGxPredict TM and/or
    FAMILION, PGxPredict:RITUXIMAB
  Pursue
    Strategic Acquisitions
    Our
    Offerings: Genetic Tests
  FAMILION PGxPredict:WARFARIN PGxPredict:CLOZAPINE PGxPredict:RITUXIMAB
  
    The FAMILION Tests  Launched in May 2004
    through our CLIA-certified laboratory in New Haven, Connecticut,
    the FAMILION suite of tests continues to reach a
    broadening market of physicians and patients in the U.S. and now
    in Europe. In July 2006, we announced the completion of our
    1,000th FAMILIONtest and in November and December 2006 announced agreements
    with Lab21 and Diagene to market and sell our FAMILIONtests in Europe. The FAMILIONtests detect mutations
    in 5 ion channel genes associated with cardiac
    channelopathies, which are rare, potentially lethal heart 10




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conditions, including Long QT Syndrome (LQT) and Brugada
    Syndrome. These conditions are caused by genetic mutations that
    result in abnormalities in the potassium and sodium channels of
    the heart and predispose affected individuals to an abnormal
    heart rhythm (arrhythmia). Familial LQT and Brugada Syndromes
    are commonly seen in apparently healthy, active adolescent
    patients. If left undiagnosed and untreated, these conditions
    can be fatal. Treatment options include life-style modification,
    the prescription or avoidance of specific classes of drugs, and
    the insertion of an implantable cardioverter/defibrillator. The
    results of these tests may assist physicians in choosing the
    most appropriate course of treatment for each patient. We have
    intellectual property rights relating to the five genes that
    have been identified as explaining the majority of two cardiac
    channelopathies, familial LQT and Brugada Syndromes, with each
    of the genes having multiple causative mutations. It is
    estimated that approximately 100,000 (1/3000) individuals in the
    U.S. have Long QT Syndrome yet many more individuals
    present every year with symptoms that could representative of
    this disease. As we discover more mutations contributing to this
    disease, the number of individuals who may be at risk increases.
    The majority of patients with LQT Syndrome are seen by a subset
    of cardiologists called electrophysiologists.  FAMILION
  2003;89:1363-1372). ® ®
    
    PGxPredict:CLOZAPINE  In January 2007, we
    announced the launch of PGxPredict:CLOZAPINE, a
    proprietary test indicated for physicians contemplating the
    initiation of clozapine treatment or for clozapine-treated
    patients whose white blood cell counts are falling. This test,
    available by prescription only, genotypes a two-SNP haplotype in
    the HLA-DQB1 gene which we have shown to be associated with
    clozapine-induced agranulocytosis in two independent cohorts.
    Clozapine-induced agranulocytosis (CIA) is a life-threatening
    decrease of white blood cells; the clozapine label requires
    frequent blood testing of patients in order to prescribe this
    drug.  ® head-to-head
 11




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American Journal of Psychiatry
  TM
  and/or
  
    PGxPredict:RITUXIMAB  In October 2006, we
    announced the in-licensing of intellectual property relating to
    the FCGRIIIa gene(encoding the Fc gamma IIIA receptor to
    which rituximab binds), a receptor for monoclonal antibodies.
    Based on this intellectual property, on January 30, 2007 we
    launched the PGxPredict:RITUXIMAB test that provides information
    on a patients likelihood of response to rituximab
    monotherapy in follicular, CD20-positive B-cell
    non-Hodgkins lymphoma. Follicular non-Hodgkins
    lymphoma, or NHL, is an indolent disease, diagnosed in
    approximately 58,000 new patients per year in the United States
    and approximately 347,00 Americans are living with NHL (Source:
    Data Monitor, 2006). Rituximab
    (Rituxan®,
    Genentech/Biogen-Idec and
    Mabthera®,
    Hoffmann-La Roche) is a monoclonal antibody used alone or
    in combination with chemotherapy to treat follicular NHL.
    However, rituximab monotherapy is only effective in 57% of
    patients and carries significant toxicity in
    57-70% of
    patients (Source:
    Rituxan®
    product insert). A four week course of rituximab treatment costs
    $10,000 to $12,000, making it a very expensive treatment with
    low efficacy and high toxicity. The test genotypes a SNP in the
    FCGRIIIa gene that results in the amino acid change of a valine
    to a phenylalanine at position 158 of the protein. This SNP has
    been functionally demonstrated to be associated to affect
    affinity of rituximab binding to the receptor. Two independent
    clinical studies have shown that patients who carry this genetic
    variant were significantly more likely to respond to rituximab
    monotherapy and that this association was robust over time,
    whether measured at three months or 12 months of treatment.
    The results of the test will identify patients as being
    More Likely or Not More Likely to
    respond. We expect to further advance this test and leverage the
    patent portfolio we in-licensed.
    PGxPredict:WARFARIN  The
    PGxPredict:WARFARINtest predicts how individual patients
    will respond to warfarin, a well-established anti-clotting agent
    often prescribed after cardiovascular events such as heart
    attack and stroke, for prophylaxis of clot formation in the
    setting of major surgery and for the treatment of other clotting
    disorders. Warfarin is the most widely used oral anti-coagulant
    in the world, and the nineteenth most prescribed drug in the
    U.S. (Source: Frost and Sullivan, 2007). It is estimated
    that there are 2 million patients on warfarin in the
    U.S. at any given time and 400,000-500,000 new patients are
    prescribed warfarin each year. Despite warfarins
    well-established efficacy, determining the correct dose can be a
    challenge as there is wide variation from patient to patient. 12




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Different patients can derive the same clinical benefit from
    dosages that differ significantly making warfarin one of the
    most difficult drugs to dose appropriately. An incorrect dose
    can lead to serious side effects, including life-threatening
    bleeding, or to recurrent clotting and disease. The optimal
    maintenance dose of warfarin for each patient is difficult to
    establish. It can take a month or more of frequent monitoring of
    the prothrombin time (known as PT, a test for blood
    coagulability) before a stable maintenance dose of warfarin is
    identified. Genetic variability in two genes, VKORC1 and CYP2C9,
    is felt to account for more than 50% of the variability in
    warfarin dosing. In November 2005, the Clinical Pharmacology
    Subcommittee of the FDAs, Advisory Committee for
    Pharmaceutical Sciences has strongly advocated for the inclusion
    of genotype information in the prescribing of warfarin. They
    agreed that (Source: Food and Drug Administrations (FDA)
    Advisory Committee for Pharmaceutical Sciences http:
    //www.fda.gov/ohrms/dockets/
    ac/05/minutes/2005-4194M1.pdf):  
    sufficient mechanistic and clinical evidence exists to use lower
    doses of warfarin for patients with genetic variations in CYP2C9
    that lead to reduced activity and genotyping patients in the
    induction phase of warfarin therapy would reduce adverse events
    and improve achievement of stable INR in patients with genetic
    variations in CYP2C9; and
    sufficient mechanistic and clinical evidence exists to use lower
    doses of warfarin for patients with genetic variations in VKORC1
    that lead to reduced VKORC1 activity and genotyping patients in
    the induction phase of warfarin therapy would reduce adverse
    events and improve achievement of stable INR in patients with
    genetic variations in VKORC1.  PGxPredict:WARFARIN.
  
    Thiopurine S-methyltransferase, or TPMT genetic
    test  The TPMT test provides a genetic assessment
    of a patients ability to metabolize the thiopurine class
    of drugs, which are commonly used in a wide range of therapeutic
    areas, including oncology, rheumatology, organ transplantation
    and vasculitis. The activity of the TPMT enzyme varies
    significantly among individuals who have different haplotypes of
    the TPMT gene. Pursuant to license agreements that we acquired
    from DNA Sciences in May 2003, we receive royalties based on net
    sales of this laboratory-developed test.    Our
    Pharmaceutical Product: Vilazodone
     13




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COGENICS
  Our
    Strategy
    Our
    Offerings
  Global
    Pharmacogenomics and Molecular Biology Services
    e-commerce
 14




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
    isolating and banking DNA and RNA samples;
    sequencing DNA samples on both the traditional (ABI3730) and
    next generation (454-Roche) automated sequencing platforms;
    performing genotyping assays on several different instrument
    platforms; which measure the genetic variation present among DNA
    samples;
    performing gene expression profiling, and confirmatory
    validation analysis on Affymetrix and Agilent microarray
    platforms and ABI QPCR instrumentation;
    providing genetic stability testing using DNA sequencing, QPCR
    and related molecular biology services for biopharmaceutical
    manufacturers;
    developing and providing laboratory-based assays to assist data
    generation and analysis during small molecule drug-based
    clinical trials as well as gene therapy and recombinant vaccine
    studies; and
    Performing metabolomics studies to generate biochemical profiles
    of samples on a liquid chromatography-mass spectrometer platform.  GLP-Compliant
    RNA and DNA Banking Services
  chain-of-custody
    Custom
    DNA Sequencing Services
    
    FDA submission quality sequencing  This
    sequencing work is designed for presentation in a report that
    can be incorporated into an application to be submitted to the
    FDA or other regulatory agencies;
    Express Sequencing  This service is designed
    to give customers a quick look at high accuracy
    double or single strand sequence data from one or multiple
    clones, in which the data is returned to the customer within a
    very short period of time after receiving the sample;
    High throughput sequencing services  This
    service involves sequencing many clones from a genomic or an
    expressed sequence tag library utilizing high-throughput
    automated systems; and
    Large scale genomic sequencing services  In
    this service, we construct libraries from a variety of genomic
    constructs and assemble them into full-length sequences, which
    can represent hundreds or 15




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thousands of genes. This can be performed using traditional
    Sanger sequencing on the ABI 3730 platform. Alternately, we can
    perform directly whole genome sequencing, Expressed Sequence Tag
    sequencing, identification of small RNAs, transcriptome
    analysis, and metagenomics on our newly acquired Roche 454 FLX
    instrument capable of generating up to 100 mega bases of
    sequencing information in a single run.  Custom
    Genotyping Services
    
    creating better informed, or smarter, clinical
    trials through the design of protocols that result in enrichment
    for response via the inclusion of those patients most likely to
    benefit from the proposed therapeutic product;
    facilitating earlier go/no-go decisions on whether
    to proceed to the next phase of clinical trial testing, which
    should result in more efficient use of clinical resources;
    reducing the size and, hence, the cost, of late-stage clinical
    trials by enrolling patients who are most likely to respond to a
    drug and/or
    are least likely to suffer an adverse reaction; and
    testing for individual susceptibility to disease or response to
    pharmaceutical treatments.    
    A broad range of platform options including genotyping by RFLP
    mapping, by mass spectrometry (Sequenom), by sequencing (ABI
    3730), by microarray (Affymetrix and Agilent) and on the Luminex
    instrument acquired in early 2007;
    A comprehensive catalog numbering in the hundreds of
    standardized genotyping assays for commonly requested SNP assays
    such as the liver drug metabolizing cytochromes and transporter
    genes. These are available for non-regulated or regulated
    environments;
    The ability to design, discover, develop and validate custom
    genotyping assays and then analyze samples with these validated
    assays on multiple platforms in non-regulated or regulated
    environments. In support of custom biomarker discovery, we may
    access our
    HAPTM
    Database, which contains highly informative, proprietary
    measures of genetic variation for more than 8,000
    pharmaceutically relevant genes;
    GLP, compliant genotyping services for assessing genomic
    variation among patients in a clinical trial, thereby permitting
    pharmaceutical and biotechnology companies to incorporate
    genomic variation information in their regulatory filings. For
    instance, we develop, validate, and run GLP-compliant genotype
    testing in support of global clinical trials (Phase I
    through Phase IV) for a wide variety of drug
    metabolism and drug target genes. GLP genotyping methods are
    developed and validated in accordance with SOPs detailing our
    formal validation program. Our GLP assays include full
    chain-of-custody
    documentation, QA data audits, and comprehensive data review to
    ensure that results are suitable for regulatory submission.
    Cogenics services in this area to date have been utilized in
    over 900 clinical trials; and
    Genotyping testing under the CLIA requirements are performed for
    the PGxHealth Division in our laboratories licensed by the
    states of Connecticut and North Carolina. Our most recent site
    audit by Connecticut CLIA was in May of 2007 where Cogenics
    performs several genotyping by sequencing tests for PGxHealth.  Gene
    Expression Profiling Services
   16




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
    We provide GLP-compliant RNA preparation, transcript profiling
    and data analysis and microarray services using Affymetrix
    Genechip®
    Gene Expression Analysis Arrays, Agilent Oligo microarrays and
    the proprietary
    MirChiptm
    technology we developed with Rosetta Genomics, as well as Laser
    Capture Micro dissection and the ability to process
    paraffin-embedded tissues on a fee-for-service basis.
    We are able to complement our microarray gene expression
    profiling service with confirmatory microarray validation
    studies using Quantitative Polymerase Chain Reaction technology
    in both unregulated and regulated environments.
    In September of 2006, Cogenics joined with other participants of
    the Micro Array Quality Control (MAQC) Consortium in publishing
    the results of the FDA-led initiative to assess the precision,
    reproducibility and comparability of microarray gene expression
    data. Cogenics contribution was unique in the generation
    and analysis of multi-platform gene expression data and resulted
    in three publications in the September 2006 issue of Nature
    Biotechnology. Cogenics is continuing to participate in the
    current MAQC Phase II study which is expanding upon the
    initial Phase I results.  Genetic
    Stability Testing Services
    
    DNA sequencing  We offer a number of
    alternative strategies to circumvent issues associated with
    having insufficient DNA and provide our clients with complete
    sequence data;.
    Copy number  A service we provide that
    monitors the number of copies of a gene contained within a cell.
    Demonstrating that cells experience predictable changes in their
    copy number during production
    scale-up
    assures regulatory authorities that the process is well
    controlled;
    Insertion number  A service that is similar to
    copy number but it is an additional analysis that is utilized to
    measure the stability of a cell bank;
    Plasmid loss or rearrangement  A plasmid is an
    artificial stretch of DNA used to insert specified genes into a
    cell. For plasmid-based gene expression systems, the loss or
    rearrangement of the plasmid can be a major practical problem in
    high yielding strains, affecting the growth of cells. We have
    assays to detect the percentage of cells that are missing or
    have undergone a loss or rearrangement of their plasmid; and
    Phage detection  Phages are bacterial viruses,
    which can kill or alter the bacteriums growth cycle or
    expression levels. Our phage detection service is designed to
    detect contamination of a bacterial cell bank. 17




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Custom
    Core Molecular Biology Services
    
    Polymerase chain reaction  known as PCR, can
    be used to amplify a specific sequence of interest from plasmid,
    viral, or genomic DNA. We also have the expertise to provide
    reverse transcription PCR for amplification of an RNA product.
    Subcloning  A procedure used to transfer a DNA
    region of interest into a vector that is more suitable for
    procedures such as DNA sequencing and gene expression. We can
    provide a strategy for subcloning a variety of different
    sequence fragments, including PCR products, into standard vector
    systems.
    Library screening  During the gene discovery
    process, customers may find only a portion of a gene of
    interest. We can use such a gene fragment to screen a library of
    clones and isolate the full-length cDNA of interest.
    Southern blot analysis  This analysis is used
    to determine the gene copy number and map the insertion location.
    DNA preparation  Many of our customers need
    large amounts of DNA for sequencing or probe generation. We have
    the ability to isolate DNA on a large-scale basis.  Metabolomics
    and Biochemical Profiling Services
  Metabolomics
    
    a research collaboration with the University of Pittsburgh
    Cancer Institute to identify biomarkers to improve the diagnosis
    of non-small cell carcinoma;
    a research collaboration with the UNC-CH and the National
    Institute or Environment Health Sciences, or NIEHS, to study the
    mechanism of acetaminophen toxicity in the liver. The research
    is focused on identifying better diagnostics for assessing liver
    damage and individual patient response to therapeutic treatment;
    a research collaboration with the Bowles Center for Alcohol
    Studies which is affiliated with UNC-CH to identify markers for
    alcohol-induced liver and brain damage and dependence, using our
    systems biology platform; and
    a master research agreement with Duke University Medical Center
    in the area of metabolomics and biomarker discovery.  Collaborations,
    Partnerships and Business Development Initiatives
   18




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Advanced
    Technology Program
    tm
    National
    Institute of Environmental Health Sciences (NIEHS)
      Medical
    Research Council
   19




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Agilent
    Technologies, Inc.
        Algynomics,
    Inc.
    VWR
    International
    Quintiles
    Transnational Corp
    Spacelabs
    Healthcare Clinical Trial Services
   20




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Roche
    Diagnostics
    Cogenics
    Market and Competition
    and/or and/or
    IVD
    TESTING  VITAL SCIENTIFIC AND ELECTA LAB
  Our
    Strategy and Markets
    near-patient/point-of-care
 21




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Our
    Products
      Clinical
    Chemistry
      
    The Vitalab Selectra-XL, a floor model 360 test per hour
    random-access, walk-away clinical chemistry analyzer
    offering a wide range of testing including clinical chemistry,
    special proteins, drugs of abuse (DOA), therapeutic drug
    monitoring (TDM), and electrolytes;
    The Vitalab Selectra E, (also trade-named Selectra II and
    Vitalab Flexor-E), a walk-away 180 test per hour
    clinical chemistry analyzer, capable of performing over 70
    different diagnostic tests using reagents from almost all
    manufacturers; 22




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
    The Vitalab Junior a walk-away 90 test per hour
    clinical chemistry analyzer, also capable of performing over 70
    different diagnostic tests using reagents from a wide range of
    producers;
    The Viva series of analyzers, dedicated systems designed for TDM
    and for the detection of DOA, which are marketed by Dade Behring
    in over thirty countries worldwide. These analyzers were
    designed specifically for use with the Dade Behring
    Emit®
    line of diagnostic assays for TDM and DOA;
    The HY-TEC 288 is a fully automated enzyme immunoassay system
    that was developed and is manufactured for Stratagene
    Corporation (formerly Hycor Biomedical, Inc.) of La Jolla,
    California. The HY-TEC 288 is a reagent system that permits the
    testing of 8 autoimmune tests and 900 allergens;
    The Vitalab 300 semi-automated clinical chemistry analyzer,
    which permits a full range of testing including endpoints,
    kinetic and bichromatic measurements; and
    A complete menu of over 20 clinical chemistry tests formulated
    and/or
    packaged by us for our range of clinical chemistry instruments.  Hematology
    tm
  
    The Excyte 10, Excyte M and Excyte M Scan which are 10
    position, random access ESR analyzers offering a range of
    functions including on-board mixing and barcode label scanning
    on the Excyte M Scan;
    The Excyte 40 and the Excyte 20 were designed for larger
    laboratories. Both feature random access, an on-board QC
    program, storage of up to 500 patient results and optional
    printer and barcode scanners. The Excyte 40 is a 40 position
    analyzer and the Excyte 20 is a 20 position analyzer; and
    The optional Excyte
    Slider®
    offers positive patient identification through all stages of
    testing.  Hemostasis
    in vitro
  Distribution
    Product
    Development
   23




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Manufacturing
    IVD
    Testing Market and Competition
        OTHER
    BUSINESS MATTERS
  Government
    Regulation
  PGxHealth
    Regulation
     24




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
    preclinical laboratory and animal tests;
    submission to the FDA of an investigational NDA, which must
    become effective before clinical trials may begin;
    adequate and well-controlled human clinical trials to establish
    the safety and efficacy of the product for its intended
    indication;
    submission to the FDA of an NDA if the FDA classifies the
    product as a new drug, or a biologic license application if the
    FDA classifies the product as a biologic; and
    FDA review of the NDA or biologic license application in order
    to determine, among other things, whether the product is safe
    and effective for its intended uses.         25




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
    the FDAs delay in granting marketing clearance or refusal
    to grant marketing clearance of a product;
    withdrawal of a product from the market; or
    the imposition of civil or criminal penalties against the
    manufacturer and holder of the marketing clearance.    In Vitro Diagnostic http://www.fda.gov/cdrh/oivd/guidance/1610.html).
      Cogenics
  Governmental
    Approval
   26




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##### Table of Contents



Governmental
    Regulations and Environmental Laws
        FAMILION
  IVD
    Testing Regulation
     27




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##### Table of Contents



Intellectual
    Property
  PGxHealth
        
    Vilazodone, our lead therapeutic product;
    detection of familial LQT Syndrome;
    detection of drug-induced LQT Syndrome;
    associations between genetic markers and drug response (efficacy
    and safety) and disease endpoints, specifically including
    rituximab response, heparin-induced thrombocytopenia, cytokine
    release syndrome, warfarin response, irinotecan response,
    clozapine-induced agranulocytosis, thiopurine metabolism, statin
    response, progression and onset of Alzheimers disease, and
    schizophrenia;
    processes for assembling genetic markers and for determining
    clinical associations; and
    coupled amplification and sequencing of DNA.    Cogenics
  Patents
    and Proprietary Technology
     28




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##### Table of Contents



IVD
    Testing
    Backlog
    Seasonality
    Employees
    Environmental
    Matters
    Significant
    Customers
    Discontinued
    Operations
   29




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##### Table of Contents



Vital
    Diagnostics
    CDSS
      ITEM 1A.
    RISK
    FACTORS    Risk
    Factors Relating to Our Business and Operations
  We do
    not have sufficient cash resources available to fund our current
    level of activities beyond the second quarter of fiscal 2008,
    including our Phase III clinical trial program for our lead
    product candidate, Vilazodone. Over the near-term, we will need
    to satisfy substantial capital requirements to pursue our
    development and commercialization strategies and to further
    optimize operations.
     30




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Given
    our current product development efforts and our recent
    acquisitions of both Genaissance Pharmaceuticals, Inc. and
    Icoria, Inc., each of which has historically incurred
    significant net losses, we expect to incur net losses for the
    foreseeable future.
      In
    previous clinical trials performed by others, Vilazodone failed
    to demonstrate significant efficacy and we may be unable to
    develop a commercially viable drug.
  and/or
  Personalized
    medicine is an emerging field, and therefore regulatory approval
    of our drug and related diagnostic tests may take longer and be
    less predictable than approval for untargeted medicines.
    Ultimately, personalized medicine may prove to be an
    unsuccessful industry, which would have a material adverse
    impact on our business and prospects.
   31




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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.
    
    establish that they are safe and effective;
    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
    can market them successfully.    We may
    not derive significant revenues from our diagnostic
    tests.
  FAMILION
 32




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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 the drug;
    published studies demonstrating the cost-effectiveness of the
    drug relative to competing products;
    development of an associated genetic screening diagnostic with
    the capability of producing accurate results;
    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 we
    are unable to develop new and enhanced products that achieve
    widespread market acceptance, we may be unable to recoup product
    development costs, and our revenues and earnings may
    decline.
    If our
    products are not granted adequate reimbursement from third-party
    payors, we may unable to successfully commercialize our products
    and we may never achieve widespread market acceptance of our
    products.
     33




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We are
    entering into new business areas and may not have the expertise,
    experience and resources to pursue all of our businesses at
    once.
    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
    recent merger activity, it may be more difficult to obtain
    additional financing at favorable terms, if at
    all.
    Because
    a significant portion of our total assets will be represented by
    goodwill that are 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.
   34




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We may
    be unable to successfully complete the integration of the
    businesses of Genaissance, Genome Express and
    Icoria.
    
    retaining existing customers and strategic partners of each
    company; 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;
    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.  As of
    March 31, 2007, we identified a material weakness in
    internal control over financial reporting, and concluded that
    our disclosure controls were not effective. If we fail to
    maintain an effective system of internal and disclosure
    controls, we may not be able to accurately report our financial
    results or prevent fraud. As a result, investors may be misled
    and lose confidence in our financial reporting and disclosures,
    and the price of our common stock may be negatively
    affected.
    Form 10-K,
   35




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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.
    We
    must implement additional and expensive finance and accounting
    systems, procedures and controls in order to grow our business
    and organization and to satisfy new reporting requirements,
    which will increase our costs and require additional management
    resources.
    In
    order to conduct clinical trials and to market our drugs, we
    will have to develop methods or make arrangements with third
    parties to produce these drugs using approved methods and at
    commercially viable rates.
   36




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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 diagnostic 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 high-density whole genome association studies to
    discover and replicate the relationship between genetic
    variations in the DNA samples and therapeutic response;
    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 marketing approvals from the FDA and other regulatory
    approvals; and
    find collaborative partners with manufacturing and commercial
    capabilities for our current and future drug candidates and
    related diagnostics. 37




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
    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
    effectiveness 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.
    Our
    international operations and sales expose us to foreign currency
    exchange rate fluctuation risks.
    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.
   38




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
    our pending patent applications may not result in issued patents;
    the claims of any issued patents may not provide meaningful
    protection;
    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.      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.
   39




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Any
    patents we obtain may be challenged by producers of generic
    drugs.
    Risk
    Factors Relating to Our Industry
  Our
    biopharmaceutical or diagnostic product candidates must undergo
    rigorous clinical trials and regulatory approvals, which could
    substantially delay or prevent their development or
    marketing.
      
    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.     40




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and/or
  Concerns
    regarding the use of genetic testing results may limit the
    commercial viability of any products we develop.
  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.
     41




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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.  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.
    
    health care and other companies that manufacture
    laboratory-based tests and analyzers;
    diagnostic and pharmaceutical companies;
    molecular services business;
    companies developing drug discovery technologies; 42




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
    companies developing molecular diagnostic and genetic
    tests; and
    companies developing point-of-care diagnostic and genetic tests.      Our
    medical device products require government approval to be
    marketed.
      Risk
    factors relating to Clinical Datas common stock
  Future
    sales of our common stock or other securities may dilute our
    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.
   43




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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, clinical trials,
    NDA filings or product approvals, contracts or acquisitions;
    variations in results of operations;
    changes in earnings estimates or other comments 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.  If the
    average closing price of our common stock were to decline
    significantly, we may be required to issue in excess of 20% of
    our outstanding capital stock upon conversion of the
    Series A Preferred Stock we issued to the preferred
    stockholder of Genaissance in our merger with that
    company.
   44




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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    ITEM 2.
    PROPERTIES    Approximate




ExpirationLocation

Square Footage


Use

DateOne Gateway Center,


6,700


Corporate office


7/31/2011Suite 702 Newton,
    Massachusetts5 Science Park


29,000


Office and laboratory


1/31/2010New Haven, Connecticut100 Perimeter Park Drive,


37,000


Office and laboratory


2/28/2015Morrisville, North Carolina9441 West Sam Houston Parkway,


15,000


Office and laboratory


12/31/2009Houston, Texas11 chemin des Pres Meylan, France


1,100


Office and laboratory


7/31/200912 chemin des Pres Meylan, France


160


Laboratory


3/31/2011Via Balzilla 41/G/4 Forli, Italy


4,800


Office, manufacturing and
    warehousing


8/31/2007Van Rensselaerweg 4 Dieren,
    The Netherlands


35,000


Office, manufacturing and
    research and development


2/1/2008Hope End, Takeley
    United Kingdom


10,000


Office and laboratory


6/30/2014     ITEM 3.
    LEGAL
    PROCEEDINGS   45




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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 Prices


DividendsHigh


Low


PaidFiscal Year Ended March 31,
    2007First Quarter

$
22.00


$
14.57


$
Second Quarter

$
16.00


$
11.45


$
Third Quarter

$
17.16


$
13.50


$
Fourth Quarter

$
22.89


$
15.96


$
Fiscal Year Ended March 31,
    2006First Quarter

$
22.00


$
13.50


$
0.04Second Quarter

$
24.71


$
17.45


$
Third Quarter

$
23.73


$
16.64


$
Fourth Quarter

$
25.87


$
17.17


$
   Holders
    of Common Stock
    Dividends
   46




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Securities
    Authorized for Issuance under Equity Compensation
    Plans
    Equity
    Compensation Plan Information
  Number of Securities to


Weighted Averagebe Issued Upon Exercise of


Exercise Price of


Number of SecuritiesOutstanding Options,


Outstanding Options,


Remaining Available forPlan Category

Warrants and Rights


Warrants and Rights


Future IssuanceEquity compensation plans approved
    by security holders


1,332,000


$
18.51



832,000Equity compensation plans not
    approved by security holders


N/A



N/A



N/ATotal


1,332,000


$
18.51



832,000       
 47




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

Date of AcquisitionGenaissance Pharmaceuticals,
    Inc.

October 6, 2005Electa Lab s.r.l

October 7, 2005Icoria, Inc.

December 20, 2005Genome Express, S.A.

March 7, 2006     Years Ended March 31,2007


2006


2005


2004


2003(In thousands, except share amounts)Consolidated Statements of
    Operations DataREVENUESServices

$
31,859


$
12,348


$



$



$
Products


31,873



25,415



24,216



21,853



13,037Total


63,732



37,763



24,216



21,853



13,037COST OF REVENUESServices


20,442



9,412











Products


20,459



16,393



16,328



15,874



9,213Total


40,901



25,805



16,328



15,874



9,213Gross profit


22,831



11,958



7,888



5,979



3,824OPERATING EXPENSESResearch and development


13,663



5,196



1,729



1,493



1,074Sales and marketing


7,924



3,255



1,681



1,294



1,181General and administrative


28,540



12,693



2,540



2,170



1,447Purchased in process research and
    development






39,700











Total operating expenses


50,127



60,844



5,950



4,957



3,702 48




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##### Table of Contents



Years Ended March 31,2007


2006


2005


2004


2003(In thousands, except share amounts)Operating (loss) income


(27,296
)


(48,886
)


1,938



1,022



122Interest expense


(627
)


(341
)


(33
)


(50
)


(28
)Interest income


475



183



60



65



43Other income (expense), net


913



(47
)


22



12



(32
)(Loss) income from continuing
    operations before taxes


(26,535
)


(49,091
)


1,987



1,049



105Provision for income taxes


(1,361
)


(1,287
)


(884
)


(124
)


(170
)(Loss) income from continuing
    operations


(27,896
)


(50,378
)


1,103



925



(65
)(Loss) income from discontinued
    operations, net of taxes


(9,626
)


(503
)


2,292



1,246



181Net (loss) income


(37,522
)


(50,881
)


3,395



2,171



116Preferred stock dividend


(104
)


(97
)










Preferred stock deemed dividend














(525
)


Net (loss) income applicable to
    common stockholders

$
(37,626
)

$
(50,978
)

$
3,395


$
1,646


$
116(Loss) income per share from
    continuing operationsBasic

$
(2.96
)

$
(8.46
)

$
0.25


$
0.15


$
(0.04
)Diluted


(2.96
)


(8.46
)


0.24



0.09



(0.03
)(Loss) income per share from
    discontinued operationsBasic

$
(1.02
)

$
(0.08
)

$
0.52


$
0.45


$
0.10Diluted


(1.02
)


(0.08
)


0.51



0.29



0.09Net (loss) income per shareBasic

$
(3.98
)

$
(8.54
)

$
0.77


$
0.60


$
0.06Diluted


(3.98
)


(8.54
)


0.75



0.51



0.06Cash dividends paid per common
    share

$



$
0.04


$
0.07


$
0.04


$
0.04Weighted average shares:Basic


9,457



5,969



4,389



2,746



1,847Diluted


9,457



5,969



4,507



4,266



1,913   March 31,2007


2006


2005


2004


2003(In thousands)Consolidated Balance Sheet
    Data:Cash and cash equivalents

$
13,949


$
7,225


$
4,171


$
1,800


$
798Total assets


87,362



108,228



39,146



38,318



11,198Long-term debt and capital leases,
    net of current portion


5,785



5,589







16



22Shareholders equity


50,592



59,789



23,809



20,264



5,346   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
 49




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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 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
       50




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Financial
    Operations Overview
  Revenues.
    Cost of Revenues.
    Research and Development Expense.
 51




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Sales and Marketing Expense.
  General and Administrative Expense.
  Purchased Research and Development
    Expense. Business
    Combinations 
  Interest and Other Income (Expense),
    Net.
  Preferred Stock Dividends.
      Critical
    Accounting Policies and Significant Judgments and
    Estimates
   52




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Form 10-K.
  Revenue Recognition 
          Allowance for Doubtful Accounts 
  Inventory Valuation  (first-in,
 53




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Valuation of Intangibles  Business
    Combinations
  Goodwill and Intangible Assets
  Accounting for the Impairment or Disposal of Long-Lived
    Assets
  Accrued Expenses 
 54




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Income Taxes 
  Results
    of Operations
  Fiscal
    Year Ended March 31, 2007 Compared to Fiscal Year Ended
    March 31, 2006
  12-month
  Revenues
    Gross Profit
    Research and Development Expense
    Sales and Marketing Expense
  General and Administrative Expense
 55




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Purchased Research and Development Expense
  Interest and Other Income (Expense), Net
      Provision For Income Taxes
  Preferred Stock Dividends
  Fiscal
    Year Ended March 31, 2006 Compared to Fiscal Year Ended
    March 31, 2005
    Revenues
      Gross Profit
 56




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Research and Development Expense
    Sales and Marketing Expense
    General and Administrative Expense
      Purchased Research and Development Expense
  Interest and Other Income (Expense), Net
      Provision For Income Taxes
  Preferred Stock Dividends
 57




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##### Table of Contents



Discontinued
    Operations
      Liquidity
    and Capital Resources
    Year end December 31,(in thousands)

2007


2006


2005Cash (used in) provided by:Operating activities

$
(12,874
)

$
(6,182
)

$
4,388Investing activities


753



(1,444
)


(930
)Financing activities


18,447



11,597



(1,386
)Effect of exchange rate


398



(917
)


299Increase in cash and cash
    equivalents

$
6,724


$
3,054


$
2,371        58




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##### Table of Contents



Payments
    Due by Period
  Fiscal 2009


Fiscal 2011Fiscal


Through


Through


AfterTotal


2008


Fiscal 2010


Fiscal 2012


Fiscal 2012(In thousands)Contractual Obligations:Short and long-term debt(1)

$
7,948


$
1,843


$
3,659


$
2,446


$
Capital lease obligations(1)


500



193



253



54



Operating lease obligations


8,393



2,169



3,303



1,295



1,626Total contractual cash obligations

$
16,841


$
4,205


$
7,215


$
3,795


$
1,626     (1)
    
    Includes interest expense           59




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and/or
    ITEM 7A.
    QUANTITATIVE
    AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK    Interest
    Rate Risk
   60




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Foreign
    Exchange
      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  Evaluation
    of Disclosure Controls and Procedures
  Rules 13a-15(b)
   61




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##### Table of Contents



Changes
    in Internal Controls
  Rules 13a-15(f) 15d-15(f)
  ITEM 9B.
    OTHER
    INFORMATION   62




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ITEM 10.
    DIRECTORS
    AND EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE  DIRECTORS
  Business Experience During Past Five Years

DirectorName and Age

and Other Directorships

SinceRandal J. Kirk
    Age: 53

Randal J. Kirk has been a director
    of Clinical Data since 2002 and Chairman of the Board of
    Directors since December 2004. Additionally, Mr. Kirk has served
    as a director of New River Pharmaceuticals Inc., a
    publicly-traded specialty pharmaceutical company focused on
    developing novel pharmaceuticals and improved versions of
    widely-prescribed drugs, since August 1996, as Chairman of its
    Board since 1996, and as its President and Chief Executive
    Officer since October 2001. Mr. Kirk has over 20 years of
    experience in the healthcare industry. Mr. Kirk began his
    professional career in the private practice of law. Mr. Kirk
    co-founded
    General Injectables & Vaccines, Inc., a pharmaceutical
    distributor (GIV), in 1983 and served as Chairman of the Board
    of GIV prior to the sale of that company in 1998. Previously,
    Mr. Kirk served as a member of the Board of Directors of Scios,
    Inc. (previously traded on the NASDAQ prior to its acquisition
    by Johnson & Johnson) between February 2000 and May 2002.
    He has served on the Board of Directors of Harvest
    Pharmaceuticals Inc., a pharmaceutical company and an affiliate
    of New River, since December 2002, and on the Virginia
    Bioinformatics Institute Policy Advisory Board since March 2004.
    Mr. Kirk also currently serves in a number of additional
    capacities with the following entities, each of which is an
    affiliate of New River: Senior Managing Director of Third
    Security, LLC, an investment management firm founded by Mr.
    Kirk, since 1999; Chairman of Biological & Popular Culture
    LLC, an automated proactive notification software and service
    company, since September 2002; and member of the Board of
    Directors of Howe and Rusling, Inc., a registered investment
    advisory firm, since December 2001. Mr. Kirk has also served on
    the Board of Visitors of Radford University since July 2003 and
    on the Board of Directors of the Radford University Foundation,
    Inc. since September 1998. Mr. Kirk received a B.A. in Business
    from Radford University and a J.D. from the University of
    Virginia.


2002Andrew J. Fromkin
    Age: 40

Andrew J. Fromkin joined Clinical
    Data on October 12, 2005, as our Executive Vice President and
    Chief Marketing Officer, and was elected President and Chief
    Executive Officer on May 12, 2006. Mr. Fromkin has more than
    17 years of senior leadership experience in the health care
    industry in the areas of corporate development, strategic
    planning, and sales and marketing management. He was most
    recently president and CEO of DoctorQuality, Inc., a leading
    provider of patient safety products and information services
    that was acquired by Quantros, Inc. Prior to that, Mr. Fromkin
    held several senior management roles at emerging healthcare
    companies, including executive appointments as President and
    Chief Executive Officer of Endo Surgical Devices, Inc., where
    his achievements included developing a line of innovative
    surgical devices, securing funding for the company, and guiding
    the company to its first FDA approval. Mr. Fromkin also was Vice
    President, Business Development and before that, Vice President,
    Sales for Merck-Medco Managed Care, LLC, a wholly owned
    subsidiary of Merck & Co., Inc. In all of these roles, Mr.
    Fromkin successfully developed and negotiated complex
    transactions including major account sales, strategic alliances,
    joint ventures and acquisitions. Mr. Fromkin began his career in
    healthcare at Health Information Technologies.


2006 63




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##### Table of Contents



Business Experience During Past Five Years

DirectorName and Age

and Other Directorships

SinceLarry D. Horner 
    Age: 73

Larry D. Horner has also served as
    a member of the Board of Directors of New River Pharmaceuticals
    Inc., a publicly-traded specialty pharmaceutical company focused
    on developing novel pharmaceuticals and improved versions of
    widely-prescribed drugs, since 1999. From 1994 to 2001, Mr.
    Horner served as Chairman of the Board of Pacific USA Holdings
    Corporation, a holding company of companies in real estate and
    financial services. From 1997 to 2001, Mr. Horner served as
    Chairman of the Board of Asia Pacific Wire & Cable, Ltd., a
    publicly-traded
    manufacturer of wire and cable products for the
    telecommunications and power industries in the Asia Pacific
    Region. From 1991 to 1994, he served as Managing Director of
    Arnhold & S. Bleichroeder, Inc., an equity market
    trading and corporate finance firm. Prior to that, he served as
    Chairman and Chief Executive Officer of the accounting firm KPMG
    Peat Marwick. Mr. Horner is on the Board of Directors of
    Atlantis Plastics, Inc., Technical Olympics USA, Inc., and
    UTStarcom, Inc., all public companies; Mr. Horner serves on the
    audit committee of all three of these companies and as the audit
    committee financial expert for Atlantis Plastics, Inc. and
    UTStarcom, Inc.


2002Arthur B. Malman 
    Age: 65

Arthur B. Malman is a partner of
    the law firm of Malman & Goldman, LLP and a principal of
    the Urban Group, a real-estate investment company. Mr. Malman is
    also Chairman of Dimex Holdings Corporation, a telecom venture
    company and a director of PS America, Inc. a floor covering
    chain. Mr. Malman received a B.A. from Princeton University and
    a J.D. from the Yale University School of Law, and attended
    Columbia University School of Business Administration.


1975Burton E. Sobel,
    M.D. 
    Age: 69

Burton E. Sobel, M.D. has
    been at the University of Vermont since 1994 where he is
    currently E.L. Amidon Professor of Medicine, Director of the
    Cardiovascular Research Institute, and Professor of
    Biochemistry. Dr. Sobel has been a trustee of Fletcher
    Allen Health Care Center in Burlington, Vermont. Previously, he
    held senior academic and administrative positions at Washington
    University School of Medicine and Barnes Hospital from 1973 to
    1994, and at the University of California, San Diego, from
    1968 to 1973. Dr. Sobel completed postgraduate training at
    the Peter Bent Brigham Hospital, Boston and the National
    Institutes of Health, Bethesda and received his M.D., magna cum
    laude, from Harvard University and his A.B. from Cornell
    University. Dr. Sobel is President-elect for the Society
    for Experimental Biology and Medicine and also serves as a
    member of the Board of Directors of Nuvelo, Inc., Ariad
    Pharmaceuticals, Inc., and New River Pharmaceuticals Inc., all
    publicly-traded life science companies


2005Kevin L. Rakin 
    Age: 46

Kevin L. Rakin is an
    Executive-In-Residence at Canaan Partners and Interim CEO of
    Advanced BioHealing, Inc. He co-founded Genaissance
    Pharmaceuticals, Inc. (acquired by Clinical Data in October
    2005) and served as its President and Chief Executive Officer
    from August 2002 until October 2005 and its President from
    October 2000. Mr. Rakin holds a B.S. in business and a M.S. in
    finance from the University of Cape Town and a M.B.A. from
    Columbia University.


2005   Board and
    Committee Matters
  Independence.
 64




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##### Table of Contents



Code of Ethics
  Audit Committee.
  EXECUTIVE
    OFFICERS
    Name

Age

PositionAndrew J. Fromkin


40


President and Chief Executive
    OfficerC. Evan Ballantyne


47


Senior Vice President and Chief
    Financial OfficerCaesar J. Belbel


47


Executive Vice President, Chief
    Legal Officer and SecretaryCarol Reed, M.D.*


54


Senior Vice President and Chief
    Medical Officer     *
    
    Significant employee  Andrew J. Fromkin
  C. Evan Ballantyne
 65




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##### Table of Contents



Caesar J. Belbel e-commerce
  Carol Reed, M.D.
  Section 16(a)
    Beneficial Ownership Reporting Compliance
    ITEM 11.
    EXECUTIVE
    COMPENSATION  COMPENSATION
    DISCUSSION AND ANALYSIS
    Compensation
    Objectives
    Elements
    of Executive Compensation
    
    base salary;
    annual cash bonus award; 66




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
    equity compensation; and
    post-termination compensation.      Base
    Salary
      Annual
    Bonus
     67




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##### Table of Contents



Equity
    Compensation
      Fringe
    Benefits
    Post-Termination
    Compensation
  gross-up
 68




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##### Table of Contents



Stock
    Option Granting Practices
    Deduction
    Limit for Executive Compensation
    COMPENSATION
    COMMITTEE REPORT:
  Form 10-K
    
 69




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##### Table of Contents



Summary
    Compensation Table
  Regulation S-K
  Summary
    Compensation Table for Fiscal Year 2007
  Option


All OtherName and Principal Position

Year(1)


Salary ($)


Bonus ($)


Awards ($)(2)


Compensation ($)(3)


Total ($)Andrew J. Fromkin,


2007



388,846



350,000



804,928



4,938



1,548,712Chief Executive Officer, 
    President,(4)C. Evan Ballantyne,


2007



143,846



90,000



84,626



1,523



319,995Chief Financial Officer, 
    Senior Vice President(5)Caesar J. Belbel,


2007



256,096



180,000



391,588







827,684Executive Vice President, 
    Secretary, General CounselIsrael M. Stein, MD,


2007



368,217







73,173



29,872



471,265former Chief Executive Officer
    
    and former Acting
    Chief Financial
    Officer(6)Mark D. Shooman,


2007



38,702











774



39,476former Chief Financial
    Officer(7)     (1)
    
    Our fiscal year ends on March 31.(2)
    
    This column represents the dollar amount recognized for
    financial statement reporting purposes with respect to the 2007
    fiscal year for the fair value of stock options granted to the
    named executive officers, in 2007 as well as prior years, in
    accordance with SFAS 123R. Portions of awards granted over
    several years are included. To see the value of awards made to
    named executive officers in fiscal 2007, see the Grants of
    Plan-Based Awards in 2007 Fiscal Year table. Pursuant to SEC
    rules, the amounts shown exclude the impact of estimated
    forfeiture related to service-based vesting conditions. For
    additional information on the valuation assumptions used by the
    Company in calculating these amounts refer to Note 14 to
    Consolidated Financial Statements included in this report. The
    amounts reported in the Summary Compensation Table for these
    awards may not represent the named executive officers will
    actually realize from the awards. Whether and to what extent, a
    named executive officer realizes value will depend on stock
    price fluctuations and the named executive officers
    continued employment. Additional information on all outstanding
    awards is reflected in the Outstanding Equity Awards at 2007
    Fiscal Year-End table.(3)
    
    The amounts set forth in the All Other Compensation column for
    the named executive officers consist of Company contributions to
    the Clinical Data 401(k) Plan. Of the amount shown for
    Dr. Stein, $5,125 constituted a car allowance and
    approximately $14,600 constituted term life insurance premiums
    and $8,300 was related to reimbursement for legal expenses.(4)
    
    Mr. Fromkin became President and Chief Executive Officer on
    May 12, 2006.(5)
    
    Mr. Ballantyne joined the Company on August 7, 2006.(6)
    
    Dr. Stein voluntarily resigned as President and Chief
    Executive Officer and became Executive Vice Chairman on
    May 12, 2006. Following the resignation of
    Mr. Shooman, he served as Acting Chief Financial Officer
    from May 30 until August 7, 2006. Subsequently,
    Dr. Stein voluntarily resigned as an officer and director
    of the Company effective as of August 30, 2006. Under the
    terms of Dr. Steins amended employment agreement with
    the Company, Dr. Stein was scheduled to receive salary
    continuation through October 28, 2007, of his then current
    base annual salary of $350,000 per year, as well as 70




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##### Table of Contents



continuation of the payment by the Company of the premiums for
    his health and dental plans, and in respect of certain life
    insurance policies maintained by the Company, together with the
    continuation his fringe benefits, including his car allowance
    for this period. On March 30, 2007, the Company terminated
    Dr. Steins amended employment agreement payment of
    all benefits payable thereunder, as a result of
    Dr. Steins alleged breach of his continuing covenants
    under the amended employment agreement. As of the date of this
    filing, no further action has been taken with respect to this
    matter by Dr. Stein or the Company.(7)
    
    Mr. Shooman voluntarily resigned his employment with the
    Company effective as of May 30, 2006. Mr. Shooman was
    not entitled to any post-termination benefits.  Grants of
    Plan-Based Awards in 2007 Fiscal Year
    All OtherOptionAwards:Number ofSecurities

Exercise or Base

Grant Date FairUnderlying

Price of Option

Value of Stock andRatification

Options

Awards

Options AwardsName

Grant Date

Date

(#)

($/Sh)

($)(3)Andrew J. Fromkin


5/12/06







150,000



18.55



2,045,4155/12/06



9/21/06
(1)


154,515



18.55



2,106,9826/22/06



9/21/06
(2)


5,303



16.10



62,943C. Evan Ballantyne


8/7/06







50,000



12.98



392,080Caesar J. Belbel


5/12/06







60,000



18.55



818,1666/22/06







3,030



16.10



35,964Israel M. Stein, MD


















Mark D. Shooman


















     (1)
    
    Options issued and granted as of May 12, 2006 and ratified
    at the annual meeting of shareholders on September 21,
    2006, vest in 36 equal monthly installments beginning on the
    first month following of the date of grant.(2)
    
    Options issued and granted as of June 22, 2006 and ratified
    at the annual meeting of shareholders on September 21,
    2006, vest equally over a three-year period beginning on the
    one-year anniversary of the date of grant.(3)
    
    This column shows the full grant date fair value of the stock
    options awarded this year under SFAS 123R. Generally, the
    full grant date fair value is the amount that the Company would
    expense in its financial statements over the awards
    vesting schedule. For stock options, fair value is calculated
    using the Black Scholes value on the grant date. The fair value
    shown is accounted for in accordance with SFAS 123R. For
    additional information on the valuation assumptions see
    Note 14 of the Consolidated Financial Statements filed as
    part of this report. 71




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Executive
    Employment Agreements
    Positions

   Mr.
    Fromkin serves as the Companys President and Chief
    Executive Officer.  Mr. Fromkin is also serving as a
    director of the Company.   Mr. Belbel
    serves as Executive Vice President, Chief Legal Officer and
    Secretary of the Company.Salary and Bonus

   Mr.
    Fromkins agreement provides for an annual base salary of
    $400,000 and a potential annual cash bonus equal to up to 200%
    of Mr. Fromkins then current annual base salary, based on
    whether Mr. Fromkin and the Company achieve certain goals, as
    determined by the board of directors in their sole discretion.   Mr.
    Belbels agreement provides for an annual base salary of
    $260,000 and a potential annual bonus equal to up to 100% of Mr.
    Belbels then current annual base salary, based on whether
    Mr. Belbel and the Company achieve certain goals, as determined
    by the board of directors in their sole discretion.Term

The initial terms of both
    employment agreements commenced on May 12, 2006 and end on June
    30, 2007, and automatically extend thereafter for successive one
    (1) year periods unless, at least ninety (90) days prior to the
    end of the initial terms or the then-current terms of the
    Agreements, the Company or the executive has notified the other
    that the term shall terminate upon its expiration date.Termination

Both agreements provide that
    employment may be terminated with or without cause at any time
    by the Company, or by the executive with or without good reason
    (as defined in the agreements).  The payments due to the
    executives upon termination by the Company without cause or by
    the executives for good reason, include continuation of the
    executives salaries for one year; continuation for one
    year of the payment of the Companys portion of the
    premiums for health and dental insurance plans; payment of
    pro-rata bonuses; and payment of accrued portions of the
    Companys contributions to any 401(k) or similar benefit
    plan.Benefits

Both executives are entitled to
    participate in all employee benefit plans of the Company and are
    entitled to four weeks vacation per year, with the ability to
    roll over up to three weeks of unused vacation from any prior
    year. The Company has agreed to provide and maintain a life
    insurance policy for Mr. Fromkin, payable to his beneficiary or
    beneficiaries, with annual premiums not to exceed $2,000.Covenants

The agreements contain
    confidentiality covenants applicable during the period of the
    executives employment and thereafter, as well as
    non-solicitation and non-competition covenants applicable to the
    executives both during and for a period of six (6) months
    following their employment with the Company.  72




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Outstanding
    Equity Awards at 2007 Fiscal Year-End
  Option AwardsNumber of


Number ofSecurities


SecuritiesUnderlying


UnderlyingUnexercised


UnexercisedOptions


Options(in #s)


(in #s)


Option Exercise


Option ExpirationName

Exercisable


Unexercisable


Price ($)


DateAndrew J. Fromkin


1,333
(1)






22.50



9/6/0850,000
(2)






17.89



10/17/1584,586
(3)


219,929
(3)


18.55



5/12/165,303
(4)


16.10



6/22/16C. Evan Ballantyne






50,000
(5)


12.98



8/7/16Caesar J. Belbel


7,500
(6)






4.82



5/7/138,000
(7)






21.34



9/23/1550,000
(2)






17.89



10/17/15



60,000
(8)


18.55



5/12/16



3,030
(9)


16.10



6/22/16Israel Stein, MD














Mark D. Shooman














     (1)
    
    Fully exercisable on the date of grant.(2)
    
    Granted on October 17, 2005, and amended to become fully
    exercisable on and after May 12, 2006.(3)
    
    Granted on May 12, 2006, and, as to 154,515 options,
    ratified on September 21, 2006, with all options vesting in
    36 equal monthly installments beginning one month after the date
    of grant. These options become fully exercisable on a change of
    control of the Company, or as a result of the termination of
    Mr. Fromkins employment by the Company without cause
    or by Mr. Fromkin for good reason.(4)
    
    Granted on June 22, 2006, and ratified on
    September 21, 2006, with one third of the options vesting
    cumulatively on each of the first three anniversaries of the
    date of grant. These options become fully exercisable on a
    change of control of the Company, or as a result of the
    termination of Mr. Fromkins employment by the Company
    without cause or by Mr. Fromkin for good reason.(5)
    
    Granted on August 7, 2006, with one third of the options
    vesting cumulatively on each of the first three anniversaries of
    the date of grant. These options become fully exercisable on a
    change of control of the Company.(6)
    
    15,000 stock options granted on May 7, 2003, with one third
    of the options vested cumulatively on each of the first three
    anniversaries of the date of grant. In fiscal 2006,
    Mr. Belbel exercised 7,500 options, leaving the balance
    shown above.(7)
    
    Granted on September 23, 2005, and amended to become fully
    exercisable on and after May 12, 2006.(8)
    
    Granted on May 12, 2006, with one third of the options
    vesting cumulatively on each of the first three anniversaries of
    the date of grant. These options become fully exercisable on a
    change of control of the Company, or as a result of the
    termination of Mr. Belbels employment by the Company
    without cause or by Mr. Belbel for good reason.(9)
    
    Granted on June 22, 2006, with one third of the options
    vesting cumulatively on each of the first three anniversaries of
    the date of grant. These options become fully exercisable on a
    change of control of the Company, or as a result of the
    termination of Mr. Belbels employment by the Company
    without cause or by Mr. Belbel for good reason. 73




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##### Table of Contents



Option
    Exercises and Stock Vested in Fiscal Year 2007
  Option AwardsNumber of Shares Acquired


ValueName

on Exercise (#)


Realized on Exercise ($)Andrew J. Fromkin






C. Evan Ballantyne






Caesar J. Belbel






Israel Stein, MD


62,000


$
683,760Mark D. Shooman


17,000


$
237,150   TERMINATION
    OF EMPLOYMENT AND CHANGE OF CONTROL ARRANGEMENTS
    (gross-up) gross-up
      Andrew J. Fromkin


Caesar J. BelbelTwelve months
    salary

$
400,000


$
260,000Twelve months health and
    other benefits


12,793



5,261Acceleration of
    options


3,061,917



854,130Tax
    gross-up


N/A



N/A  74




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##### Table of Contents



DIRECTOR
    COMPENSATION IN FISCAL YEAR 2007
    Title

Cash Compensation


Equity Compensation (See below)Chairman

$
60,000 per year



20,000 stock optionsDirector

$
30,000 per year



10,000 stock options        75




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##### Table of Contents



Fees Earned or Paid

Restricted Stock

Option AwardsName

in Cash ($)

Awards ($)(1)

($)(2)

Total ($)Randal J. Kirk, Chair


60,000



168,892







228,892Larry D. Horner


34,000







139,181



142581Arthur B. Malman


34,000



84,446







118,446Burton E. Sobel MD


34,000







139,181



142,581Kevin L. Rakin(4)


28,080







1,015,649



1,043,729Joseph Klein III(3)










40,576



40,576     (1)
    
    This column represents the dollar amount recognized for
    financial statement reporting purposes with respect to the 2007
    fiscal year for the fair value of restricted stock units
    (RSUs) granted to directors in 2007 as well as prior
    years. In fiscal 2007, Messrs. Kirk and Malman received
    RSUs totaling 10,800 and 5,400, respectively.(2)
    
    This column represents the dollar amount recognized for
    financial statement reporting purposes with respect to the 2007
    fiscal year for the fair value of stock options granted to
    directors, in 2007 as well as prior years, in accordance with
    SFAS 123R. Pursuant to SEC rules, the amounts shown exclude
    the impact of estimated forfeiture related to service-based
    vesting conditions. For additional information on the valuation
    assumptions used by the Company in calculating these amounts
    refer to Note 14 to Consolidated Financial Statements included
    in this report. For fiscal 2007, Mr. Horner, Dr. Sobel
    and Mr. Rakin each elected to receive options to purchase
    10,000 shares, for which the grant date fair value was
    $14.80.(3)
    
    Mr. Klein was a director through September 21, 2006.
    Because Mr. Klein elected in fiscal 2006 to receive his
    cash and equity compensation for his service as a director
    during that fiscal year, in the form of deferred stock units for
    his cash compensation and restricted stock units for his equity
    compensation, Mr. Klein received 1,518 shares of
    unrestricted Common Stock on March 28, 2007 in respect of
    his deferred stock units.(4)
    
    In May 2006, the Company granted 70,000 options to Kevin Rakin,
    a member of the Companys Board of Directors, in connection
    with the settlement of an employment agreement. The options were
    exercisable immediately and had a fair value of approximately
    $896,000, which was expensed on the date of grant. On
    September 21, 2007, Mr. Rakin received 4,360 options
    related to his duties as a Board member in fiscal 2006, which
    were immediately exercisable. On the same day, Mr. Rakin
    received an additional 10,000 options in connection with
    his duties as a member of the Board of Directors for fiscal 2007.  ITEM 12.
    SECURITY
    OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND
    RELATED STOCKHOLDER MATTERS  EQUITY
    COMPENSATION PLAN INFORMATION
    Number of Securities RemainingNumber of Securities to be


Weighted-Average Exercise


Available for Future Issuance UnderIssued Upon Exercise of


Price of Outstanding


Equity Compensation Plans (ExcludingOutstanding Options


Options


Securities Reflected in Column (a))Plan Category

(a)


(b)


(c)Equity compensation plans approved
    by security holders


1,332,000


$
18.51



832,000Equity compensation plans not
    approved by security holders


N/A



N/A



N/ATotal


1,332,000


$
18.51



832,000  76




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##### Table of Contents



SECURITY
    OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
      Stock and Nature of

Percent ofName and Address of Beneficial Owner(1)

Ownership

Common Stock5% StockholderThird Security, LLC and affiliates


4,028,656
(2)


40.00
%The Governor Tyler
    1881 Grove Avenue
    Radford, VA 24141Directors, Executive Officers
    and Significant EmployeeRandal J. Kirk


4,028,656
(2)


40.00
%Arthur B. Malman


43,325
(3)


*Larry D. Horner


91,279
(4)


*Burton E. Sobel, M.D.


15,000
(5)


*Kevin L. Rakin


117,036
(6)


1.15
%Andrew J. Fromkin


172,672
(7)


1.69
%Caesar J. Belbel


86,510
(8)


*Carol Reed, M.D.


81,434
(9)


*C. Evan Ballantyne


1,000



*Israel M. Stein, M.D.


421,836
(10)


4.19
%Mark D. Shooman


3,000



*All Directors, Current Executive
    Officers and Significant Employee as a Group (9 persons)


4,636,912
(11)


43.80
%     *
    
    Indicates ownership of less than 1%(1)
    
    The address of each of the directors, named executive officers
    and executive officers is:
    c/o Clinical
    Data, Inc., One Gateway Center, Suite 702, Newton, MA
    02458, other than Dr. Stein, whose address is 17 Edge Hill
    Road, Chestnut Hill, Massachusetts 02467; and Mr. Shooman,
    whose address is 1460 Beacon Street, Waban, Massachusetts 02468.(2)
    
    Includes 1,066,991 shares owned by Mr. Kirk;
    680,504 shares owned by Kirkfield, LLC; 731,083 shares
    owned by RJK, LLC; 41,719 shares owned by Zhong Mei, LLC;
    699,918 shares owned by New River Management, II, LP;
    193,343 shares owned by New River Management, III, LP;
    153,353 shares owned by Radford Investment LP; and
    461,745 shares owned by Third Security Staff 2001 LLC.
    Mr. Kirk is deemed to have beneficial ownership of all
    shares owned by Kirkfield, LLC, RJK, LLC, Zhong Mei, LLC, New
    River Management, II, LP, New River Management, III,
    LP, Radford Investment LP and Third Security Staff 2001,
    LLC.(3)
    
    Includes 24,000 shares issuable upon the exercise of stock
    options exercisable within 60 days after June 8, 2007
    and 2,500 shares issuable upon the exercise of warrants for
    shares of common stock.(4)
    
    Includes 14,218 shares held by Mr. Horners wife
    as to which Mr. Horner disclaims beneficial ownership. Also
    includes 39,000 shares issuable upon the exercise of stock
    options exercisable within 60 days after June 8, 2007
    and 9,609 shares issuable upon the exercise of warrants for
    shares of common stock by Mr. Horner and 7,109 shares
    issuable upon the exercise of warrants for shares of common
    stock by Mr. Horners wife.(5)
    
    Consists of 15,000 shares issuable upon the exercise of
    stock options exercisable within 60 days after June 8,
    2007. 77




---



##### Table of Contents



(6)
    
    Includes 6,175 shares held in trust and 325 shares
    held jointly with Mr. Rakins wife. Also includes
    79,360 shares issuable upon the exercise of stock options
    exercisable within 60 days after June 8, 2007 and
    1,250 shares issuable upon the exercise of warrants for
    shares of common stock.(7)
    
    Includes 163,063 shares issuable upon the exercise of stock
    options exercisable within 60 days after June 8, 2007.(8)
    
    Consists of 86,510 shares issuable upon the exercise of
    stock options exercisable within 60 days after June 8,
    2007.(9)
    
    Includes 79,809 shares issuable upon the exercise of stock
    options exercisable within 60 days after June 8, 2007.(10)
    
    Based on the latest data available to us. Dr. Stein is no
    longer serving as our Chief Executive Officer and has no
    reporting responsibility.(11)
    
    See footnotes (2) through (9), including
    Mr. Ballantynes shares.  ITEM 13.
    CERTAIN
    RELATIONSHIPS AND RELATED TRANSACTIONS AND INDEPENDENT
    DIRECTORS           78




---



##### Table of Contents



ITEM 14.
    PRINCIPAL
    ACCOUNTANT FEES AND SERVICES      2007


2006Audit Fees(1)

$
656,689


$
688,907Audit-Related Fees(2)


52,782



108,458Tax Fees(3)


116,453



107,142Total

$
825,924


$
904,508     (1)
    
    Audit fees represent fees for professional services provided in
    connection with the audit of our financial statements and review
    of our quarterly financial statements and audit services
    provided in connection with other statutory or regulatory
    filings.(2)
    
    Audit-related fees represent payments for due diligence services
    provided in connection with certain business combinations.(3)
    
    Tax fees represent fees for services rendered to us for tax
    compliance services and related consultations.       79




---



##### Table of Contents



PART IV  ITEM 15.
    EXHIBITS,
    FINANCIAL STATEMENT SCHEDULES           80




---



##### Table of Contents



SIGNATURES      
        
          
       
       
      81




---



##### Table of Contents



82




---



##### 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, 2007 and 2006


F-3Consolidated
    Statements of Operations for the Years Ended March 31,
    2007, 2006 and 2005


F-4Consolidated
    Statements of Stockholders Equity for the Years Ended
    March 31, 2007, 2006 and 2005


F-5Consolidated
    Statements of Cash Flows for the Years Ended March 31,
    2007, 2006 and 2005


F-6Notes to
    Consolidated Financial Statements


F-8  F-1




---



##### Table of Contents



REPORT
    OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM           Share Based
    Payment
        F-2




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  CONSOLIDATED
    BALANCE SHEETS
   March 31,2007


2006(In thousands, except share and per share amounts)ASSETSCurrent Assets:Cash and cash equivalents

$
13,949


$
7,225Accounts receivable, net


11,053



11,566Inventories


7,910



7,843Prepaid expenses and other current
    assets


2,625



4,693Assets of discontinued operations


9,466



12,467Total current assets


45,003



43,794Property, plant and equipment, net


6,791



8,250Goodwill


20,126



21,197Intangible assets, net


12,636



22,595Other assets, net


724



1,268Assets of discontinued operations


2,210



11,123TOTAL ASSETS

$
87,490


$
108,227LIABILITIES AND
    STOCKHOLDERS EQUITYCurrent Liabilities:Current portion of long-term debt

$
1,404


$
3,155Current portion of capital leases


171



226Accounts payable


6,787



8,660Accrued expenses


8,081



13,132Customer advances and deferred
    revenue


1,921



2,147Other current liabilities


1,503



1,971Liabilities of discontinued
    operations


8,118



9,655Total current liabilities


27,985



38,946Long-Term Liabilities:Long-term debt, net of current
    portion


5,506



5,518Capital lease obligations, net of
    current portion


279



71Other long-term liabilities


2,032



2,186Liabilities of discontinued
    operations


968



1,717Total long-term liabilities


8,785



9,492Commitments and contingencies
    (Note 10)






Stockholders Equity:Preferred Stock, $.01 par
    value, 1,500,000 shares authorized, 484,070 authorized
    Series A voting, convertible preferred stock, 184,000 and
    234,000 shares issued and outstanding at March 31,
    2007 and 2006, liquidation preference of $4,343 at
    March 31, 2007


2



2Common stock, $.01 par value,
    14,000,000 shares authorized; 10,022,000 and
    8,520,000 shares issued at March 31, 2007 and 2006,
    respectively; 10,012,000 shares and 8,510,000 shares
    outstanding at March 31, 2007 and 2006, respectively


100



85Additional paid-in capital


132,435



105,145Accumulated deficit


(83,436
)


(45,810
)Treasury stock, 10,000 shares
    at cost


(47
)


(47
)Deferred compensation






(318
)Accumulated other comprehensive
    income


1,666



732Total stockholders equity


50,720



59,789TOTAL LIABILITIES AND
    STOCKHOLDERS EQUITY

$
87,490


$
108,227    F-3




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  CONSOLIDATED
    STATEMENTS OF OPERATIONS
  Years Ended March 31,2007


2006


2005(In thousands, except per share amounts)REVENUESServices

$
31,859


$
12,348


$
Products


31,873



25,415



24,216Total


63,732



37,763



24,216COST OF REVENUESServices


20,442



9,412



Products


20,459



16,393



16,328Total


40,901



25,805



16,328Gross profit


22,831



11,958



7,888OPERATING EXPENSES:Research and development


13,663



5,196



1,729Sales and marketing


7,924



3,255



1,681General and administrative


28,540



12,693



2,540Purchased in process research and
    development






39,700



Total operating expenses


50,127



60,844



5,950Operating (loss) income


(27,296
)


(48,886
)


1,938Interest expense


(627
)


(341
)


(33
)Interest income


475



183



60Other income (expense), net


913



(47
)


22(Loss) income from continuing
    operations before taxes


(26,535
)


(49,091
)


1,987Provision for income taxes


(1,361
)


(1,287
)


(884
)(Loss) income from continuing
    operations


(27,896
)


(50,378
)


1,103(Loss) income from discontinued
    operations, net of taxes


(9,626
)


(503
)


2,292Net (loss) income


(37,522
)


(50,881
)


3,395Preferred stock dividend


(104
)


(97
)


Net (loss) income applicable to
    common stockholders

$
(37,626
)

$
(50,978
)

$
3,395(Loss) income per share from
    continuing operationsBasic

$
(2.96
)

$
(8.46
)

$
0.25Diluted

$
(2.96
)

$
(8.46
)

$
0.24(Loss) income per share from
    discontinued operationsBasic

$
(1.02
)

$
(0.08
)

$
0.52Diluted

$
(1.02
)

$
(0.08
)

$
0.51Net (loss) income per shareBasic

$
(3.98
)

$
(8.54
)

$
0.77Diluted

$
(3.98
)

$
(8.54
)

$
0.75Weighted average shares basic


9,457



5,969



4,389Weighted average shares diluted


9,457



5,969



4,507    F-4




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  CONSOLIDATED STATEMENTS OF STOCKHOLDERS
    EQUITY
 FOR THE YEARS ENDED MARCH 31, 2007, 2006 AND 2005
  Common





(Accumulated








AccumulatedPreferred


Preferred


Common


Stock


Additional


Deficit)








OtherStock


Stock Par


Stock


Par


Paid-In


Retained


Treasury


Deferred


Comprehensive





ComprehensiveShares


Value


Shares


Value


Capital


Earnings


Stock


Compensation


Income


Total


(Loss) Income(In thousands)BALANCE at April 1, 2004










4,405


$
44


$
16,995


$
2,303


$
(56
)





$
978


$
20,264Exercise of stock options


























9











9Dividends paid






















(354
)














(354
)Translation adjustment


































495



495


$
495Net income






















3,395















3,395



3,395Total comprehensive income









































$
3,890BALANCE at March 31, 2005










4,405



44



16,995



5,344



(47
)






1,473



23,809Series A preferred stock
    issued in connection with acquisitions


484



5











9,512



















9,517Conversion of Series A
    preferred stock into common stock


(250
)


(3
)


250



3























Equity issued in connection with
    acquisitions










3,040



30



62,504











(572
)






61,962Exercise of stock options










42







331



















331Private placement of equity, net of
    transaction costs of $83










614



6



11,930



















11,936Exercise of stock warrants










153



2



3,587



















3,589Issuance of restricted stock










16







286











(143
)






143Dividends paid on common stock






















(176
)














(176
)Dividends accrued on preferred stock






















(97
)














(97
)Amortization of deferred
    compensation






























397







397Translation adjustment


































(741
)


(741
)

$
(741
)Net loss






















(50,881
)














(50,881
)


(50,881
)Total comprehensive loss









































$
(51,622
)BALANCE at March 31, 2006


234



2



8,520



85



105,145



(45,810
)


(47
)


(318
)


732



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


(50
)






50



























Adoption of FAS 123R


















(318
)










318







Exercise of stock options










102



1



574



















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










1,040



10



16,846



















16,856Exercise of stock warrants










191



2



3,703



















3,705Dividends accrued on preferred stock






















(104
)














(104
)Issuance of common stock for the
    purchase of Vilazodone rights










103



1



1,622



















1,623Purchase of treasury stock


























(234
)










(234
)Retirement of treasury stock










(16
)






(234
)






234











Issuance of warrants


















120



















120Equity issued in connection with
    the Genome Express acquisition










15







347



















347Stock based compensation










17



1



4,630



















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



10,022


$
100


$
132,435


$
(83,436
)


(47
)






1,666



50,720    F-5




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
 CONSOLIDATED
    STATEMENTS OF CASH FLOWS Years Ended March 31,2007


2006


2005(In thousands)CASH FLOWS FROM OPERATING
    ACTIVITIES:Net (loss) income

$
(37,522
)

$
(50,881
)

$
3,395Less (loss) income from
    discontinued operations


(9,626
)


(503
)


2,292Net (loss) income from continuing
    operations


(27,896
)


(50,378
)


1,103Adjustments to reconcile net
    (loss) income from continuing operations to net cash (used in)
    provided by operating activities:Depreciation and amortization


10,266



4,984



376Purchased research and development






39,700



Impairment of intangible assets


2,583







Stock-based compensation including
    Merck license


6,120



540



Gain on sale of investment


(890
)






(Gain) loss on sales of equipment


(41
)


26



(10
)Deferred taxes


(218
)


(18
)


178Changes in current assets and
    liabilities:Accounts receivable


1,063



(498
)


1,364Inventories


510



(2,163
)


281Prepaid expenses and other current
    assets


2,152



943



229Other assets


616



(218
)


(32
)Accounts payable and accrued
    liabilities


(5,981
)


4,456



162Customer advances and deferred
    revenue


(460
)


891



(45
)Other current liabilities


(1,774
)


(2,944
)


360Cash (used in) provided by
    continuing operations


(13,950
)


(4,676
)


3,966Cash provided by (used in)
    discontinued operations


1,076



(1,503
)


422Net cash (used in) provided by
    operating activities


(12,874
)


(6,182
)


4,388CASH FLOWS FROM INVESTING
    ACTIVITIES:Purchases of equipment


(1,230
)


(1,023
)


(410
)Proceeds from sale of investment


1,000







Proceeds from sales of equipment


393



78



26Cash used in business combinations


(222
)


(322
)


Capitalization of software
    development costs






(175
)


(247
)Cash used in investing
    activities  continuing operations


(59
)


(1,442
)


(631
)Cash provided by (used in)
    investing activities  discontinued operations


812



(2
)


(299
)Net cash used in investing
    activities


753



(1,444
)


(930
) F-6




---



##### Table of Contents



Years Ended March 31,2007


2006


2005(In thousands)CASH FLOWS FROM FINANCING
    ACTIVITIES:Borrowings under other debt
    arrangements


121



121



Payment on debt and capital leases


(2,233
)


(7,291
)


(22
)Proceeds from the sale of common
    stock and warrants, net of transaction costs


20,561



15,525



Purchase of treasury shares


(234
)






Exercise of stock options


575



331



9Stockholder dividends






(231
)


(354
)Cash provided by financing
    activities  continuing operations


18,790



8,455



(367
)Cash (used in) provided by
    financing activities  discontinued operations


(343
)


3,142



(1,019
)Net cash provided by financing
    activities


18,447



11,597



(1,386
)EFFECT OF EXCHANGE RATE CHANGES ON
    CASH AND CASH EQUIVALENTS


398



(917
)


299NET INCREASE IN CASH AND CASH
    EQUIVALENTS


6,724



3,054



2,371CASH AND CASH EQUIVALENTS,
    BEGINNING OF PERIOD


7,225



4,171



1,800CASH AND CASH EQUIVALENTS, END OF
    PERIOD

$
13,949


$
7,225


$
4,171Supplemental disclosure of cash
    flow information:Cash paid during the year for:Interest

$
916


$
341


$
33Income taxes

$
865


$
1,331


$
2,028Non-cash transactions:Accrued acquisition costs

$



$
60


$
Equity issued in business
    acquisitions

$
219


$
71,479


$
Debt issued in business
    acquisitions

$



$
607


$
Equipment acquired through capital
    leases and long-term debt

$
279


$



$
Equity issued to acquired
    technology rights

$
1,623


$



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

$
120


$



$
Accrued preferred stock dividends

$
146


$
42


$
     F-7




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL STATEMENTS
 FOR THE YEARS ENDED MARCH 31, 2007, 2006 AND 2005
  (1)
    Nature of
    Business and Basis of Presentation  Nature
    of Business
    TM
  TM
  in vitro
    Basis
    of Presentation
    and/or
 F-8




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    (2)
    Significant
    Accounting Policies  Principles
    of Consolidation
    Use
    of Estimates
    Cash
    and Cash Equivalents
    Accounts
    Receivable
      2007


2006


2005(In thousands)Allowance for uncollectible
    accounts  beginning of year

$
884


$
381


$
165Provisions


130



752



216Less: deductions


(133
)


(249
)


Allowance for uncollectible
    accounts  end of year

$
881


$
884


$
381   Inventories
    (first-in,
 F-9




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        2007


2006(In thousands)Raw materials

$
4,680


$
5,131Work-in-process


1,486



1,457Finished goods


1,744



1,255$
7,910


$
7,843   Depreciation
    and Amortization
    Asset Classification

Useful LivesManufacturing and computer
    equipment

3-7 yearsLaboratory equipment

2-7 yearsLeasehold improvements

Lesser of useful life or lease termFurniture and fixtures

2-7 yearsVehicles

3-5 years     Goodwill
    and Intangibles
    Goodwill and other Intangible Assets
 F-10




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Accounting for the Impairment or Disposal of Long-Lived
    Assets
  Software
    Development Costs
  Accounting for the Costs of Computer
    Software to be Sold, Leased or Otherwise Marketed
      Warranties
      2007


2006


2005(In thousands)Accrued warranty 
    beginning of year

$
290


$
227


$
240Assumed during the purchase of
    Electa Lab






25



Provisions


163



104



12Less: warranty claims


(54
)


(66
)


(25
)Accrued warranty  end
    of year

$
399


$
290


$
227  F-11




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Derivatives
    Revenue Recognition
            Research
    and Development Costs
   F-12




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Income
    Taxes
    Comprehensive
    (Loss) Income
    Foreign
    Currency
    Net
    (Loss) Income per Share
      2007


2006


2005(In thousands)Basic weighted average common
    shares outstanding


9,457



5,969



4,389Dilutive effect of common stock
    options










118Dilutive weighted average common
    shares outstanding


9,457



5,969



4,507  F-13




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2007


2006(In thousands)Common stock options


1,340



612Common stock warrants


789



452Convertible note payable


89



95Restricted common stock


8



16Convertible Series A
    preferred stock


184



234Total


2,410



1,409   Equity-Based
    Compensation
  Share-Based Payment Accounting for Stock
    Issued to Employees Accounting for Stock-Based Compensation
  Concentration
    of Credit Risk
    Fair
    Value of Financial Instruments
    Recent
    Accounting Pronouncements
  Accounting for Uncertainty in Income Taxes an
    interpretation of FAS 109 Accounting for
    Income Taxes
 F-14




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Fair Value
    Measurements
  The
    Fair Value Option for Financial Assets and Financial
    Liabilities  Iincluding an amendment of FASB
    Statement No. 115 Fair Value Measurements
  (3)
    Discontinued
    Operations    Vital
    Diagnostics
    CDSS
   F-15




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      2007


2006


2005(In thousands)Revenues

$
24,761


$
30,985


$
32,184(Loss) income From Operations
    Before Disposal:(Loss) income before taxes and
    minority interest

$
(2,348
)

$
461


$
3,542Minority interest


(9
)


(19
)


(16
)(Loss) income before taxes


(2,357
)


442



3,526Income taxes


(91
)


(945
)


(1,234
)(Loss) income from discontinued
    operations before disposal, net of taxes


(2,448
)


(503
)


2,292Disposal:Loss on disposal before taxes


(7,178
)






Income tax benefit










Loss on disposal, net of taxes


(7,178
)






(Loss) income from discontinued
    operations, net of tax

$
(9,626
)

$
(503
)

$
2,292  F-16




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2007


2006(In thousands)Cash and equivalents

$
122


$
Accounts receivable, net


4,007



5,725Inventory, net


5,188



6,246Prepaid expenses and other current
    assets


149



496Property, plant and equipment, net


1,906



2,656Other assets


304



8,467Assets of discontinued operations

$
11,676


$
23,590Revolving credit facility

$
3,970



3,980Current portion of capital leases
    and long-term debt


496



548Accounts payable


1,716



2,178Customer advances


1,000



269Other accrued expenses


936



2,680Capital leases and long-term debt,
    net of current portion


814



1,474Other long-term liabilities


154



243Liabilities of discontinued
    operations

$
9,086


$
11,372   (4)
    Business
    Combinations  Genaissance
    Pharmaceuticals,
    Inc.
       F-17




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    (In thousands)Value of the Companys common
    stock

$
45,570Value of the Companys
    Series A preferred stock


9,517Fair value of stock options and
    warrants


2,846Transaction costs


1,248Less: cash acquired


(978
)$
58,203       Purchase Price Allocation (In thousands)Accounts receivable

$
4,717Inventories


517Other current assets


1,269Equipment


6,040Intangible assets


53,150Long-term assets


373Accounts payable


(1,621
)Current portion of long-term debt
    and capital lease obligations


(5,104
)Accrued expenses and other current
    liabilities


(8,217
)Long-term debt and capital lease
    obligations


(3,338
)Long-term liabililties


(1,593
)Deferred compensation for unvested
    options, restricted common stock and warrants


521Goodwill


11,489Total purchase price

$
58,203  F-18




---



##### Table of Contents



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


AverageValue


Useful Life(In thousands)Completed technology

$
9,000



4.6 yearsIn-process research and development


36,300Customer relationships


7,500



7.9 yearsOther


350



3.9 years$
53,150   Electa
    Lab
    s.r.l.
        Purchase Price Allocation (In thousands)Cash

$
214Accounts receivable


217Inventories


554Other current assets


10Equipment


310Long-term assets


2Accounts payable


(260
)Accrued expenses and other current
    liabilities


(275
)Goodwill


1,153Total purchase price

$
1,925   Icoria,
    Inc.
     F-19




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Black-Scholes
    (In thousands)Value of the Companys common
    stock

$
11,329Fair value of stock options and
    warrants


308Transaction costs


367Less: cash acquired


(1,901
)$
10,103       Purchase Price Allocation (In thousands)Accounts receivable

$
2,603Inventories


329Other current assets


2,360Equipment


1,715Intangible assets


10,500Long-term assets


667Accounts payable


(780
)Current portion of long-term debt
    and capital lease obligations


(3,010
)Accrued expenses and other current
    liabilities


(5,705
)Long-term debt and capital lease
    obligations


(2,531
)Deferred compensation for unvested
    options, restricted common stock and warrants


52Goodwill


3,903Total purchase price

$
10,103  F-20




---



##### Table of Contents



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


AverageValue


Useful Life(In thousands)Completed technology

$
3,400



7.6 yearsIn-process research and development


3,400Customer relationships


3,300



5.3 yearsOther


400



3.0 years$
10,500   Genome
    Express
    S.A.
      (In thousands)Value of the Companys common
    stock

$
2,485Value of the Companys
    contingently issuable common stock


361Transaction costs


490Less: cash acquired


(9
)$
3,327    F-21




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Purchase Price Allocation (In thousands)Accounts receivable

$
599Inventories


146Other current assets


887Equipment


726Long-term assets


18Accounts payable


(438
)Current portion of long-term debt
    and capital lease obligations


(629
)Accrued expenses and other current
    liabilities


(1,618
)Long-term debt


(1,016
)Goodwill


4,652Total purchase price

$
3,327     Restructuring
    and Integration Reserves
    Restructuring





Balance








Balanceand Integration





March 31,


Fiscal 2007


March 31,Reserves


Payments


2006


Accrual


Payments


2007Severance

$
3,098


$
(748
)

$
2,350


$
125


$
(2,265
)

$
210Lease termination costs


1,495



(405
)


1,090







(1,090
)


$
4,593


$
(1,153
)

$
3,440


$
125


$
(3,355
)

$
210   In-Process
    Research and Development
    project-by-project
   F-22




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      
    Clozapine:  In December 2004, Genaissance
    reported the discovery of genetic markers that are believed to
    predict who is at risk of developing Clozapine-induced
    agranulocytosis, a life threatening decrease of white blood
    cells that requires frequent blood testing of patients.
    Genaissance is in the process of organizing another clinical
    trial to further support its findings. This IPRD project was
    estimated to be 60% complete as of the acquisition date. The
    estimated fair value of this IPRD project was $17.9 million
    as of October 6, 2005.
    Vilazodone:  In September 2004, Genaissance
    acquired an exclusive license from Merck KGaA (Merck) to develop
    and commercialize Vilazodone, which is under development for the
    treatment of depression. Genaissance is attempting to identify
    the genetic marker that defines patients who are more likely to
    respond to Vilazodone and develop a genetic test. This project
    was estimated to be 25% complete as of the acquisition date. The
    estimated fair value of this IPRD project was $18.4 million
    as of October 6, 2005.
    Acute liver injury and liver-disease-related research projects:
    Icoria had several research projects underway to identify
    biomarkers. These projects were estimated to be 75% complete
    relative to Icorias role. The estimated fair value of
    these IPRD projects was $3.4 million as of
    December 20, 2005.       F-23




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (5)
    Property,
    Plant and Equipment    2007


2006(In thousands)Manufacturing, computer equipment
    and software

$
7,503


$
5,940Leasehold improvements


3,836



3,398Laboratory equipment


3,413



3,506Furniture and fixtures


797



1,157Vehicles


8



715,557



14,008Less: accumulated depreciation and
    amortization


8,766



5,758$
6,791


$
8,250     (6)
    Goodwill
    and Intangible Assets    Clinics & Small


MolecularHospitals


Services


Total(In thousands)Balance at March 31, 2005

$



$



$
Additions:Electa Lab


1,153







1,153Genaissance






11,489



11,489Icoria






3,903



3,903Genome Express






4,652



4,652Balance at March 31, 2006


1,153



20,044



21,197Adjustments:Genaissance






(1,210
)


(1,210
)Icoria






(238
)


(238
)Genome Express






377



377Balance at March 31, 2007

$
1,153


$
18,973


$
20,126    F-24




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Goodwill and Other
    Intangible Assets
    2007


2006(In thousands)Purchased intangibles:Completed technology

$
9,210


$
12,400Customer relationships


10,800



10,800Other


570



76920,580



23,969Less: accumulated amortization


(8,854
)


(2,921
)Purchased intangibles, net


11,726



21,048Capitalized software


1,761



1,609Less: accumulated amortization


(851
)


(443
)Capitalized software, net


910



1,166ERP implementation and software






381Intangible assets, net

$
12,636


$
22,595       (7)
    Other
    Assets    2007


2006(In thousands)Restricted cash

$
224


$
785Deposits


301



231Other


199



252$
724


$
1,268    F-25




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (8)
    Accrued
    Expenses    2007


2006(In thousands)Payroll and payroll-related
    expenses

$
3,812


$
2,721Commissions, royalties and license
    fees


1,002



1,002Accrued professional fees


621



644Unvouchered invoices


419



439Accrued severance and other
    acquisition costs


348



4,180Accrued dividends assumed in
    acquisition






1,211Warranty reserve


239



290Accrued facilities costs


307



1,138Accrued VAT and sales taxes


189



236Other


1,144



1,271$
8,081


$
13,132   (9)
    Debt  Long-term
    Debt
    2007


2006(In thousands)Notes payable, bearing interest at
    6.5%, with maturities between February 2009 and May 2011 and
    secured by certain of Cogenics leasehold improvements

$
3,033


$
3,520Convertible note payable, bearing
    interest at 10.75% at March 31, 2007 with maturity on
    October 19, 2010; secured by all of Icorias assets


2,570



3,227Advances from French government
    under a program to stimulate national innovation, with
    maturities between September 2007 and September 2008


1,123



1,134Euro note payable, bearing
    interest at 5.5%, with maturity on September 2007 and quarterly
    payments of $76 and secured by a bank guarantee


166



452Other note payable


18



3406,910



8,673Less: current portion


(1,404
)


(3,155
)$
5,506


$
5,518    F-26




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      2008

$
1,4042009


1,6112010


1,5222011


2,1562012


217After


Total

$
6,910     (10)
    Commitments
    and Contingencies   F-27




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Contractual
    Commitments and Commercial Obligations
    Operating


CapitalizedYear Ending March 31,

Leases


Leases2008

$
2,169


$
1932009


1,800



1652010


1,503



882011


698



332012


597



21Thereafter


1,626



Total

$
8,393



500Less: amount representing interest






(50
)Total principal obligations






450Less: current portion






(171
)Long-term capital lease





$
279       (11)
    Significant
    Customers    (12)
    Equity  Preferred
    Stock
    Dividends 
 F-28




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Voting 
  Conversions 
    Redemption  wound-up, 2 3 and/or
  Common
    Stock
     F-29




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
          (13)
    Income
    Taxes    2007


2006


2005(In thousands)United States

$
(30,848
)

$
(52,958
)

$
(668
)Foreign


4,313



3,867



2,655$
(26,535
)

$
(49,091
)

$
1,987     2007


2006


2005(In thousands)Current:Federal

$



$
(73
)

$
(143
)State


189



33



(4
)Foreign


1,390



1,345



853Total Current


1,579



1,305



706Deferred:Federal


(492
)


9



(56
)State


(28
)


18



Foreign


(116
)


(48
)


103Change in valuation allowance


418



3



131Total Deferred


(218
)


(18
)


178$
1,361


$
1,287


$
884  F-30




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2007


2006


2005(In thousands)(Benefits from) provision for
    taxes at statutory rate

$
(9,022
)

$
(16,524
)

$
869Losses not benefited


9,849



3,898



Prior losses utilized


(224
)






State taxes


116



33



(4
)Non-US rate differential, net


(136
)


(128
)


(13
)Change in valuation reserves


418



3



132Write-off of purchased research
    and development






13,498



Other


360



507



(100
)$
1,361


$
1,287


$
884     2007


2006(In thousands)Deferred tax assets:Net operating losses

$
135,115


$
128,404Capitalized research costs


9,933



9,738Tax credits


4,322



2,413Fixed assets


2,113



1,916Severance and accrued payroll


1,725



740Other reserves and accrued
    liabilities


2,586



720Total assets


155,794



143,931Deferred tax liabilities:Purchased intangibles


(4,400
)


(7,750
)Capitalized software


(328
)


(448
)Other






(22
)Total liabilities


(4,728
)


(8,220
)Net deferred tax asset


151,066



135,711Less: valuation allowance


(151,318
)


(136,015
)$
(252
)

$
(304
)   Accounting for Income Taxes
   F-31




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      (14)
    Stock
    Incentive Plans and Equity Based Compensation         F-32




---



##### 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, 2004


199


$
5.58Exercised


(11
)


1.63Outstanding March 31, 2005


188



5.82Granted


304



18.54Issued in connection with business
    combinations


392



62.82Forfeited


(230
)


55.14Exercised


(42
)


7.93Outstanding March 31, 2006


612



30.17Granted


1,084



16.77Forfeited


(254
)


23.65Exercised


(102
)


5.24Outstanding March 31, 2007


1,340


$
18.27



8.7 years


$
5,476Exercisable March 31, 2007


427


$
21.33



7.5 years


$
1,762Exercisable March 31, 2006


242


$
26.25Available for future grants
    March 31, 2007


904     $4.6 million
   F-33




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2007(In thousands, exceptper share amounts)Cost of revenues

$
146Sale and marketing


533Research and development


99General and administrative


3,719Pre-tax stock based compensation
    expense

$
4,497Income tax benefits


Stock based compensation expense,
    net

$
4,497Basic and diluted net loss per
    share

$
0.48             2007

2006Risk-free interest rate

4.00-5.18%

3.88-4.75%Expected dividend yield

0.00%

0.00%Expected lives

5-6 years

3-5 yearsExpected volatility

73-82%

32-43%Weighted average grant date fair
    value

$10.33

$30.17    F-34




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2006


2005(In thousands, except per share amounts)Net (loss) income applicable to
    common stockholders, as reported

$
(50,978
)

$
3,395Add: Stock-based employee
    compensation expense included in reported net loss


540



Deduct: Total stock-based
    compensation expense determined under the fair value method


(889
)


(108
)Pro forma net (loss) income
    applicable to common stockholders

$
(51,327
)

$
3,287As reportedBasic loss per share

$
(8.54
)

$
0.77Diluted loss per share

$
(8.54
)

$
0.75Pro-formaBasic loss per share

$
(8.60
)

$
0.75Diluted loss per share

$
(8.60
)

$
0.73     OutstandingWeightedAverage


Weighted





WeightedRemaining


Average


Exercisable


AverageNumber of


Contractual


Exercise


Number of


ExercisePrice Range

Shares


Life


Price


Shares


Price(Thousands)


(Years)





(Thousands)$ 4.82 - 6.31


38



2.43


$
4.98



38


$
4.98$ 7.85 - 9.20


16



6.61



9.08



16



9.08$11.00 - 13.23


66



7.92



12.58



15



11.27$13.85 - 15.46


293



9.34



14.77



20



14.81$16.00 - 18.55


852



9.17



17.93



287



18.24$18.92 - 22.50


35



8.34



21.70



23



21.88$23.84 - 28.99


6



7.38



25.70



4



25.76$30.46 - 35.43


9



7.68



33.80



4



33.77$39.30 - 41.23


13



6.64



39.41



10



39.41$46.15 - 190.77


12



5.61



74.93



10



81.681,340



8.72


$
18.27



427


$
21.33   (15)
    Defined
    Contribution and Pension Plans   F-35




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  (16)
    Segment
    Information  Disclosures about Segments of an
    Enterprise and Related Information
      Clinics andMolecular

SmallServices

Hospitals

All Other

Total(In thousands)Revenues2007

$
31,557


$
32,175


$



$
63,7322006


12,332



25,407



24



37,7632005






24,135



81



24,216Cost of revenues and operating
    expenses2007

$
55,652


$
27,967


$
7,409


$
91,0282006


62,322
(a)


21,730



2,597



86,6492005






21,275



1,003



22,278Interest expense2007

$
539


$
31


$
57


$
6272006


256



32



53



3412005






7



26



33Interest income2007

$
85


$
68


$
322


$
4752006


29



91



63



1832005






60







60Income tax (benefit) provision2007

$
126


$
(1,168
)

$
(319
)

$
(1,361
)2006


199



(1,435
)


(51
)


(1,287
)2005






(859
)


(25
)


(884
)(Loss) income from continuing
    operations2007

$
(24,636
)

$
3,202


$
(6,462
)

$
(27,896
)2006


(50,520
)


2,596



(2,454
)


(50,378
)2005






1,872



(769
)


1,103     (a)
    
    Includes $39,700 of purchased research and development costs
    written off after the acquisitions of Genaissance on
    October 6, 2005 and Icoria on December 21, 2005.  F-36




---



##### Table of Contents



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


Small





DiscontinuedServices


Hospitals


All Other


Operations


Total(In thousands)Capital expenditures2007

$
914


$
276


$
40



n/a


$
1,2302006


104



915



4



n/a



1,0232005






404



6



n/a



410Total assets2007

$
47,280


$
20,373


$
8,033


$
12,232


$
87,9182006


63,127



18,108



3,403



23,590



108,228     NorthAmerica


Europe


Asia


All Other


Consolidated(In thousands)Revenues2007

$
24,486


$
23,635


$
7,645


$
7,966


$
63,7322006


10,767



16,365



6,345



4,286



37,7632005


867



13,217



6,469



3,663



24,216Property Plant &
    Equipment, net2007

$
4,396


$
2,395


$



$



$
6,7912006


5,698



2,552











8,250Goodwill & Intangibles,
    net2007

$
24,922


$
7,840


$



$



$
32,7622006


35,656



8,136











43,792   (17)
    Related
    Party Transactions       F-37




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        (18)
    Subsequent
    Events      (19)
    Quarterly
    Summarized Financial Information (Unaudited)  First

Second

Third

FourthQuarter 2007

Quarter 2007

Quarter 2007

Quarter 2007(1,2)(In thousands except per share amounts)Total revenues

$
17,649


$
13,993


$
16,181


$
15,909Gross profit


2,750



4,903



5,631



9,547Operating loss


(5,260
))


(7,552
)


(5,943
)


(8,541
)Loss from continuing operations


(5,707
)


(7,789
)


(5,363
)


(9,037
)Loss from discontinued operations


(478
)


(331
)


(909
)


(7,908
)Net loss


(6,185
)


(8,120
)


(6,272
)


(16,945
)Net loss per share:Basic and diluted

$
(0.71
)

$
(0.85
)

$
(0.65
)

$
(1.76
)     (1)
    
    Loss from continuing operations includes a $2.6 million
    impairment charge relating to intangible assets at Icoria. F-38




---



##### Table of Contents



CLINICAL
    DATA, INC. AND SUBSIDIARIES
  NOTES TO
    CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
   (2)
    
    The loss from discontinued operations includes a disposal loss
    of $7.0 million related to the reduction of the carrying
    value of CDSS to fair value.  First


Second


Third


FourthQuarter 2006


Quarter 2006


Quarter 2006(3)


Quarter 2006(4)Total revenues

$
4,821


$
5,608


$
12,200


$
15,134Gross profit


1,743



2,023



5,298



2,894Operating income (loss)


326



552



(42,432
)


(7,332
)Income (loss) from continuing
    operations


188



306



(42,870
)


(8,002
)Income (loss) from discontinued
    operations


220



71



152



(946
)Net income (loss)


408



377



(42,718
)


(8,948
)Net income (loss) per share:Basic

$
0.09


$
0.09


$
(6.25
)

$
(1.10
)Diluted

$
0.09


$
0.08


$
(6.25
)

$
(1.10
)   (3)
    
    For the three months ended December 31, 2005, includes
    $40,100 of purchased research and development costs related to
    the acquisition of Genaissance on October 6, 2005 and
    Icoria on December 20, 2005.(4)
    
    For the three months ended March 31, 2006, includes $400
    adjustment to the value of the purchased research and
    development costs related to the acquisition of Genaissance on
    October 6, 2005. F-39




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##### Table of Contents



EXHIBIT INDEX
  ExhibitNumber

Description2
.1

Amended and Restated Agreement and
    Plan of Merger, dated as of April 29, 2003, among Clinical
    Data, Landmark and Spectran. Filed as Exhibit 2.1 to the
    Companys Current Report on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.2

Agreement and Plan of Merger,
    dated as of April 29, 2003, among CDSS, GPSI and Clinical
    Data. Filed as Exhibit 2.2 to the Companys Current
    Report on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.3

Asset Purchase Agreement, dated as
    of December 9, 2002, among Elan Pharmaceuticals, Inc.,
    Elan, CDSS and Clinical Data. Filed as Exhibit 2.1 to
    the Companys Current Report on
    Form 8-K,
    as filed with the Commission on December 9, 2002, and
    incorporated herein by reference.2
.4

Amendment No. 1 to Original
    Asset Purchase Agreement, dated as of February 10, 2003,
    among Elan Pharmaceuticals, Inc., Elan, CDSS and Clinical Data.
    Filed as Exhibit 2.4 to the Companys Current Report
    on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.5

Amendment No. 2 to Original
    Asset Purchase Agreement, dated as of March 18, 2003, among
    Elan Pharmaceuticals, Inc., Elan, CDSS and Clinical Data.
    Filed as Exhibit 2.5 to the Companys Current Report
    on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.6

Amendment No. 3 to Original
    Asset Purchase Agreement, dated as of March 31, 2003, among
    Elan Pharmaceuticals, Inc., Elan, CDSS and Clinical Data.
    Filed as Exhibit 2.6 to the Companys Current Report
    on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.7

Amendment No. 4 to Original
    Asset Purchase Agreement, dated as of April 29, 2003, among
    Elan Pharmaceuticals, Inc., Elan, CDSS and Clinical Data.
    Filed as Exhibit 2.7 to the Companys Current Report
    on
    Form 8-K,
    as filed with the Commission on May 12, 2003, and
    incorporated herein by reference.2
.8

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
.9

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
.10

Agreement and Plan of Merger,
    dated as of September 19, 2005, among Clinical Data, Inc.,
    Irides Acquisition Corporation and Icoria, Inc. Filed as
    Exhibit 2.1 to the Companys Current Report on
    Form 8-K,
    as filed with the Commission on September 22, 2005, and
    incorporated herein by reference.3
.1

Certificate of Incorporation.
    Filed as Exhibit 3.1 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.3
.2

Certificate of Amendment of
    Certificate of Incorporation filed with the Secretary of State
    of the State of Delaware on October 1, 2003. Filed as
    Exhibit 3.1 to the Companys Quarterly Report on
    Form 10-Q,
    as filed with the Commission on February 17, 2004, and
    incorporated herein by reference.3
.3

Certificate of Elimination of the
    Series A Nonvoting Convertible Preferred Stock filed with
    the Secretary of State of the State of Delaware on July 7,
    2005. Filed as Exhibit 3.1 to the Companys Current
    Report on
    Form 8-K,
    as filed with the Commission on July 11, 2005, and
    incorporated herein by reference.3
.4

Certificate of Designation of the
    Series A Preferred Stock filed with the Secretary of State
    of the State of Delaware on October 4, 2005. Filed as
    Exhibit 3.2 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 11, 2005, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description3
.5

Certificate of Amendment of
    Certificate of Incorporation filed with the Secretary of State
    of the State of Delaware on October 6, 2005. Filed as
    Exhibit 3.1 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on October 11, 2005, and
    incorporated herein by reference.3
.6

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 Series A Preferred
    Stock Certificate. Filed as Exhibit 4.2 to the
    Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 29, 2006, and
    incorporated herein by reference.10
.1

1991 Directors Option
    Plan and Forms of Option Agreement. Filed as Exhibits to the
    Companys Registration Statement on
    Form S-8,
    filed with the Commission on March 5, 1992, and
    incorporated herein by reference.10
.2

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
.3

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
.4

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
.5

Amended and Restated 2005 Equity
    Incentive Plan. Filed as Exhibit 10.3 to the Companys
    Quarterly Report on
    Form 10-Q,
    filed with the Commission on November 14, 2006, and
    incorporated herein by reference.10
.6

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
.7*

Employment Agreement of Israel M.
    Stein dated October 29, 2001. Filed as Exhibit 10.3 to
    the Companys Quarterly Report on
    Form 10-QSB,
    filed with the Commission on February 14, 2002, and
    incorporated herein by reference.10
.8*

Amendment No. 1 dated
    December 16, 2004 to Employment Agreement of Israel M.
    Stein dated October 29, 2001. Filed as Exhibit 10.1 to
    the Companys Current Report on
    Form 8-K,
    filed with the Commission on December 22, 2004, and
    incorporated herein by reference.10
.9*

Amendment No. 2 dated
    July 10, 2006 to Employment Agreement of Israel M. Stein
    dated October 29, 2001. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on July 14, 2006, and
    incorporated herein by reference.10
.10*

Amendment No. 3 dated
    August 31, 2006 to Employment Agreement of Israel M. Stein
    dated October 29, 2001. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.11*

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.10
.12*

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
.13*

Employment Offer Letter between
    the Company and C. Evan Ballantyne dated August 7, 2006.
    Filed as Exhibit 10.2 to the Companys Quarterly
    Report on
    Form 10-Q,
    filed with the Commission on November 14, 2006, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description10
.14*

Form of Amended and Restated
    Indemnification Agreement between the Company and Israel M.
    Stein, M.D. and Arthur Malman, respectively. 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
.15*

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
.16

Loan and Security Agreement, dated
    March 31, 2003, among LaSalle, as lender, and CDSS,
    BioClinical Concepts, Inc. and GSPI Acquisition, Inc. as
    Borrowers. Filed as Exhibit 10.1 to the Companys
    Current Report on
    Form 8-K,
    filed with the Commission on May 12, 2003, and incorporated
    herein by reference.10
.17

$10,000,000 Demand Revolving Note,
    dated March 31, 2003, issued by CDSS in favor of LaSalle.
    Filed as Exhibit 10.3 to the Companys Current Report
    on
    Form 8-K,
    filed with the Commission on May 12, 2003, and incorporated
    herein by reference.10
.18

Amendment No. 3 to Loan and
    Security Agreement, dated November 12, 2003, among LaSalle,
    CDSS, BioClinical Concepts, Inc. and GSPI Acquisition, Inc.
    Filed as Exhibit 10.5 to the Companys Quarterly
    Report on
    Form 10-QSB,
    filed with the Commission on November 14, 2003, and
    incorporated herein by reference.10
.19

Amendment No. 5 to Loan and
    Security Agreement, dated October 25, 2004, among LaSalle,
    as lender, and Clinical Data Sales & Service, Inc., as
    borrower. Filed as Exhibit 10.2 to the Companys
    Quarterly Report on
    Form 10-QSB,
    filed with the Commission on February 11, 2005, and
    incorporated herein by reference.10
.20

Amendment No. 6 to Loan and
    Security Agreement, dated January 28, 2005, among LaSalle,
    as lender, and Clinical Data Sales & Service, Inc., as
    borrower. Filed as Exhibit 10.10 to the Companys
    Annual Report on
    Form 10-KSB,
    filed with the Commission on June 27, 2005, and
    incorporated herein by reference.10
.21

Amendment No. 7 to Loan and
    Security Agreement, dated as of December 2, 2005, between
    Clinical Data Sales & Service, Inc. and La Salle
    Business Credit, LLC. Filed as Exhibit 10.11 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on February 14, 2006, and
    incorporated herein by reference.10
.22

Investor Rights Agreement, dated
    as of June 20, 2005, between the Company and RAM Trading,
    Ltd. Filed as Exhibit 99.1 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on June 24, 2005, and
    incorporated herein by reference.10
.238

Form of Securities Purchase
    Agreement among the Company and the Investors listed therein,
    dated as of November 17, 2005. Filed as Exhibit 99.1
    to the Companys Current Report on
    Form 8-K,
    filed with the Commission on November 21, 2005, and
    incorporated herein by reference.10
.24

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
.25

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
.26

Omnibus Amendment dated
    August 31, 2006, by and among the Company, Icoria, Inc. and
    Laurus Master Fund, Ltd. Filed as Exhibit 99.2 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.27

Securities Purchase Agreement, by
    and between Icoria, Inc. and Laurus Master Fund, Ltd., dated as
    of October 19, 2004. Filed as Exhibit 10.5 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on February 14, 2006, and
    incorporated herein by reference.10
.28

Amended and Restated Securities
    Purchase Agreement dated August 31, 2006 to Securities
    Purchase Agreement, by and between Icoria, Inc. and Laurus
    Master Fund, Ltd., dated as of October 19, 2004. Filed as
    Exhibit 99.3 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.




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##### Table of Contents



ExhibitNumber

Description10
.29

Master Security Agreement, by and
    between Icoria, Inc. and Laurus Master Fund, Ltd., dated as of
    October 19, 2004. Filed as Exhibit 10.6 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on February 14, 2006, and
    incorporated herein by reference.10
.30

Amended and Restated Master
    Security Agreement dated August 31, 2006 to Master Security
    Agreement, by and between Icoria, Inc. and Laurus Master Fund,
    Ltd., dated as of October 19, 2004. Filed as
    Exhibit 99.5 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.31

Registration Rights Agreement, by
    and between Icoria, Inc. and Laurus Master Fund, Ltd., dated as
    of October 19, 2004. Filed as Exhibit 10.7 to the
    Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on February 14, 2006, and
    incorporated herein by reference.10
.32

Registration Rights Agreement, by
    and between the Company and Laurus Master Fund, Ltd., dated as
    of August 31, 2006. Filed as Exhibit 99.7 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.33

Form of Two Year Common Stock
    Purchase Warrant, dated as of August 31, 2006. Filed as
    Exhibit 99.8 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.34

Form of Transferor Endorsement
    dated August 31, 2006. Filed as Exhibit 99.9 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.35

Amended and Restated Secured
    Convertible Term Note dated August 31, 2006 to Secured
    Convertible Term Note, by and between Icoria, Inc. and Laurus
    Master Fund, Ltd., dated as of October 19, 2004. Filed as
    Exhibit 99.4 to the Companys Current Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.36

Guaranty dated August 31,
    2006. Filed as Exhibit 99.6 to the Companys Current
    Report on
    Form 8-K,
    filed with the Commission on September 7, 2006, and
    incorporated herein by reference.10
.37

Form of Securities Purchase
    Agreement among the Company and the Investors, dated as of
    June 13, 2006. Filed as Exhibit 99.1 to the
    Companys Current Report on
    Form 8-K,
    filed with the Commission on June 15, 2006, and
    incorporated herein by reference.10
.38

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
.39

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
.40

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
.41*

Letter Agreement between the
    Companys subsidiary, Genaissance Pharmaceuticals, Inc.,
    and Kevin Rakin, a director of the Company. Filed as
    Exhibit 10.31 to the Companys Annual Report on
    Form 10-K,
    filed with the Commission on June 29, 2006, and
    incorporated herein by reference.10
.42

Selective Share Buy-Back Agreement
    among Vital Diagnostics Pty. Ltd., Clinical Data, B.V., and
    Clinical Data, Inc. (with respect to Sections 4.4, 6 and 7
    only) dated November 13, 2006. Filed as Exhibit 10.1
    to the Companys Quarterly Report on
    Form 10-Q,
    filed with the Commission on November 14, 2006, 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.




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##### Table of Contents



ExhibitNumber

Description31
.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.