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UNITED STATES SECURITIES AND
    EXCHANGE COMMISSIONWashington, D.C.
    20549
  Form 10-K
  (Mark One)þ

ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
    SECURITIES EXCHANGE ACT OF 1934For the fiscal year ended
    December 31, 2008oro

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
    SECURITIES EXCHANGE ACT OF 1934For the transition period
    from          to   Commission file number
    000-49839
 Idenix Pharmaceuticals,
    Inc.
 (Exact Name of Registrant as
    Specified in its Charter)
  Delaware

45-0478605(State or Other Jurisdiction
    of

(I.R.S. EmployerIncorporation or
    Organization)

Identification No.)60 Hampshire Street,Cambridge, Massachusetts

02139(Address of Principal Executive
    Offices)

(Zip Code)  (617) 995-9800
 (Registrants telephone
    number, including area code)
  Securities registered pursuant to Section 12(b) of the
    Act:
  Common Stock, $.001 par value

The NASDAQ Global Market(Title of class)

(Name of exchange on which
    registered)   Securities registered pursuant to Section 12(g) of the
    Act:
 NONE
  o þ
  o þ
  þ o
  Regulation S-K Form 10-K Form 10-K. o
  12b-2
  Large
    accelerated
    filer o
    Accelerated
    filer þ
    Non-accelerated
    filer o
    Smaller reporting
    company o (Do not check if a smaller
    reporting company)
  Rule 12b-2 o þ
      DOCUMENTS
    INCORPORATED BY REFERENCE
  Form 10-K.




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Idenix
    Pharmaceuticals, Inc.
  Form 10-K
  TABLE OF
    CONTENTS
   
 PART IItem 1.


Business


4Item 1A.


Risk Factors


22Item 1B.


Unresolved Staff Comments


44Item 2.


Properties


44Item 3.


Legal Proceedings


44Item 4.


Submission of Matters to a Vote of Security
    Holders


44PART IIItem 5.


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


44Item 6.


Selected Consolidated Financial Data


45Item 7.


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


46Item 7A.


Quantitative and Qualitative Disclosure about
    Market Risk


63Item 8.


Financial Statements and Supplementary Data


63Item 9.


Changes in and Disagreements with Accountants on
    Accounting and Financial Disclosure


63Item 9A.


Controls and Procedures


64Item 9B.


Other Information


65PART IIIItem 10.


Directors, Executive Officers and Corporate
    Governance


66Item 11.


Executive Compensation


66Item 12.


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


66Item 13.


Certain Relationships, Related Transactions and
    Director Independence


66Item 14.


Principal Accountant Fees and Services


66PART IVItem 15.


Exhibits and Financial Statement Schedules


67SIGNATURES


104Exhibit Index


105EX-10.28 License Agreement, dated February 4, 2009EX-10.35 Amendment Agreement, dated February 4, 2009EX-10.46 Agreement, dated December 3, 2008EX-10.55 Amendment No. 1 to Employment Agreement, dated December 23, 2008EX-21.1 Subsidiaries of the CompanyEX-23.1 Consent of PricewaterhouseCoopers LLPEX-31.1 CEO Cert Section 302EX-31.2 CFO Cert Section 302EX-32.1 CEO Cert Section 906EX-32.2 CFO Cert Section 906   2




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Cautionary
    Statement Regarding Forward-Looking Statements
  Form 10-K Form 10-K Form 10-K Form 10-K.
  Form 10-K
  Form 10-K Form 10-K Form 10-K
 3




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PART I  Item 1.
    Business.  Overview
  ® ®
  Hart-Scott-Rodino
        ® ® ® ®
 4




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Available
    Information
  Form 10-K. Form 10-K, Form 10-Q, Form 8-K www.sec.gov. at 1-800-SEC-0330.
  617-995-9800. Form 10-K
  Products
    and Drug Candidates
    Hepatitis
    C
  HCV
    Discovery Program
    first-in-man once-per-day,
   5




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HIV
  once-a-day
  10 10
   6




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Hepatitis
    B
  ® ®
  Antiviral
    Research
    Our Scientists.
  Focused Compound Library.
  Target Selection.
  Screening.
  Pharmacology, Preclinical Development and Lead
    Optimization. in vitro in
    vivo in vivo in vitro in vivo
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Collaboration
    and License Agreements
  Novartis
    Collaboration
    
    the development and commercialization agreement, under which we
    collaborate with Novartis to develop, manufacture and
    commercialize our drug candidates which they license from us;
    the supply agreement, under which Novartis manufactured for us
    the active pharmaceutical ingredient, or API, for the clinical
    development and commercial supply of drug candidates it licensed
    from us and the finishing and packaging of licensed products for
    commercial sale;
    the stockholders agreement, which was subsequently amended
    and restated in July 2004 in connection with the closing of our
    initial public offering; and
    the stock purchase transaction, under which Novartis purchased
    approximately 54% of our outstanding capital stock from our then
    existing stockholders for $255.0 million in cash, with an
    additional aggregate amount of up to $357.0 million
    contingently payable to these stockholders if we achieve
    predetermined milestones with respect to the development of
    specific HCV drug candidates, including valopicitabine (a drug
    candidate we ceased developing in July 2007) and prodrugs.    Development
    and Commercialization Agreement
  Designation
    of Products
  ® ® ® ®
    Development
    of Products and Regulatory Activities
   8




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Product
    Commercialization
        Indemnification
    Termination
    
    with respect to the particular product, drug candidate or
    country to which the breach relates; or
    in its entirety, if the material breach is not limited to a
    particular product, drug candidate or country.   9




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##### Table of Contents



Master
    Manufacturing and Supply Agreement
    Stockholders
    Agreement
    
    granted Novartis, together with certain other holders of our
    common stock, rights to cause us to register, under the
    Securities Act of 1933, as amended, such shares of common stock;
    agreed to use our reasonable best efforts to nominate for
    election as a director at least two designees of Novartis for so
    long as Novartis and its affiliates own at least 35% of our
    voting stock and at least one designee of Novartis for so long
    as Novartis and its affiliates own at least 19.4% of our voting
    stock; and
    granted Novartis approval rights over a number of corporate
    actions that we or our subsidiaries may take as long as Novartis
    and its affiliates continue to own at least 19.4% of our voting
    stock.  Novartis
    Stock Purchase Rights
    Stock
    Purchase Agreement
     10




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GlaxoSmithKline
    Collaboration
    
    a license agreement whereby we granted GSK an exclusive license
    to develop, manufacture and commercialize our NNRTI compounds,
    including IDX899, for the treatment of human diseases, including
    HIV/AIDS, on a worldwide basis; and
    a stock purchase agreement under which GSK will purchase
    2,475,728 shares of our common stock at an aggregate
    purchase price of $17.0 million, or a per share price of
    $6.87.        
    by mutual written agreement of the parties;
    by either party if a closing does not occur within 90 days
    following the filings made in connection with the HSR
    clearance; or 11




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
    by either us or GSK in the event that a governmental entity
    issues a final and nonappealable order, decree or injunction or
    takes any action to restrain, enjoin or prohibit the
    transactions contemplated by the GSK stock purchase agreement.            
    consented to the sale by us of the 2,475,728 shares to GSK;
    approved entering into the GSK license agreement;
    waived its rights to buy a pro rata portion of the shares issued
    to GSK;
    approved our granting of registration rights to GSK and waived
    its rights to participate in such registration; and
    waived, until a certain time, its rights to request that we file
    a registration statement on Novartis behalf or include
    shares of our common stock owned by Novartis in any such
    registration statement filed on behalf of GSK.       12




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Cooperative
    Laboratory Agreements
  CNRS
    and the University of Montpellier
    University
    of Cagliari
     13




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Research
    and Development Expenses
    ® ®
  Manufacturing
        Sales and
    Marketing
   14




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Patents
    and Licenses
      Hepatitis
    B Patent Portfolio and Licenses
      
    U.S. Patent No. 6,395,716 entitled
    ß-L-2-Deoxy-Nucleosides for the Treatment of
    Hepatitis B;
    U.S. Patent No. 6,569,837 entitled
    ß-L-2-Deoxy Pyrimidine Nucleosides for the
    Treatment of Hepatitis B;
    U.S. Patent No. 6,444,652 entitled
    ß-L-2-Deoxy-Nucleosides for the Treatment of
    Hepatitis B; and
    U.S. Patent No. 6,566,344, entitled
    ß-L-2-Deoxy-Nucleosides for the Treatment of
    Hepatitis B.        ® ®
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##### Table of Contents



Hepatitis
    C Patent Portfolio
      HIV
    Patent Portfolio
        Competition
    
    product effectiveness;
    safety;
    timing and scope of regulatory approvals;
    price of products;
    availability of supply;
    patent protection; and
    sales and marketing capabilities and resources.   16




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® ®
  ® ® ® ® 2-a
    Pharmaceutical
    Pricing and Reimbursement
      Regulatory
    Matters
   17




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® ® ® ® ®
  FDA
    Requirements for Approval of Drug Products
    
    product seizures;
    voluntary or mandatory recalls;
    voluntary or mandatory patient and physician notification;
    withdrawal of product approvals;
    restrictions on, or prohibitions against, marketing our
    products, if approved for commercial sale;
    fines;
    restrictions on importation of our products;
    injunctions;
    debarment;
    civil and criminal penalties; and
    suspension of review, refusal to approve pending applications.    in vitro
  30-day 30-day
 18




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6-month
     19




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and/or and/or
  and/or
      Foreign
    Regulation of Drug Product Approval
    Europe
    Mutual Recognition Procedure and Decentralized
    Approval.
 20




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Centralized Procedure.
    Asia
    Marketing
    Applications Format
  e-CTDs,
  Hazardous
    Materials
   21




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Employees
    Item 1A.
    Risk
    Factors  Form 10-K
  Factors
    Related to Our Business
  We
    have a limited operating history and have incurred a cumulative
    loss since inception. If we do not generate significant
    revenues, we will not be profitable.
  ® ® and/or
  We
    will need additional capital to fund our operations, including
    the development, manufacture and potential commercialization of
    our drug candidates. If we do not have or cannot raise
    additional capital when needed, we will be unable to develop and
    ultimately commercialize our drug candidates
    successfully.
  ® ®
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
    with respect to IDX899, whether GSK is able to continue
    preclinical and clinical development of this drug candidate such
    that we receive certain preclinical and clinical development
    milestone payments within the next 24 months;
    with respect to our other drug candidates, Novartis exercises
    its option to license other drug candidates, and we receive
    related license fees, milestone payments and development expense
    reimbursement payments from Novartis; and with respect to our
    other drug candidates not licensed by Novartis, we receive
    related license fees, milestone payments and development expense
    reimbursement payments from third parties; and
    with respect to
    Tyzeka®/Sebivo®,

    whether the level of royalty payments received from Novartis is
    significant.      
    the amount of revenue that we may be able to realize from
    commercialization and sale of drug candidates, if any, which are
    approved for commercial sale by regulatory authorities;
    the scope and results of our preclinical studies and clinical
    trials;
    the progress of our current preclinical and clinical development
    programs for HCV and HIV (to the extent that the GSK license
    agreement does not become effective);
    the cost of obtaining, maintaining and defending patents on our
    drug candidates and our processes;
    the cost, timing and outcome of regulatory reviews;
    the commercial potential of our drug candidates;
    the rate of technological advances in our markets;
    the cost of acquiring or in-licensing new discovery compounds,
    technologies, drug candidates or other business assets;
    the magnitude of our general and administrative expenses;
    any costs we may incur under current and future licensing
    arrangements; and
    the costs of commercializing and launching other products, if
    any, which are successfully developed and approved for
    commercial sale by regulatory authorities.  and/or
     23




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Our
    research and development efforts may not result in additional
    drug candidates being discovered on anticipated timelines, if at
    all, which could limit our ability to generate
    revenues.
    Our
    failure to successfully acquire or develop and market additional
    drug candidates or approved drugs would impair our ability to
    grow.
        Our
    investments are subject to general credit, liquidity, market and
    interest rate risks, which may be exacerbated by the volatility
    in the U.S. credit markets.
    The
    markets which we intend to enter are subject to intense
    competition. If we are unable to compete effectively, products
    we successfully develop and our drug candidates may be rendered
    noncompetitive or obsolete.
   24




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® ®
    
    significantly greater financial, technical and human resources
    than we have and may be better equipped to discover, develop,
    manufacture and commercialize products;
    more extensive experience in conducting preclinical studies and
    clinical trials, obtaining regulatory approvals and
    manufacturing and marketing pharmaceutical products;
    products that have been approved or drug candidates that are in
    late-stage development; and
    collaborative arrangements in our target markets with leading
    companies and research institutions.    and/or
  ® ®
    If we
    are not able to attract and retain key management and scientific
    personnel and advisors, we may not successfully develop our drug
    candidates or achieve our other business
    objectives.
   25




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Our
    business has a substantial risk of product liability claims. If
    we are unable to obtain or maintain appropriate levels of
    insurance, a product liability claim against us could adversely
    affect our business.
    ® ® ® ® ® ®
  Our
    insurance policies are expensive and protect us only from some
    business risks, which will leave us exposed to significant,
    uninsured liabilities.
    If the
    estimates we make, and the assumptions on which we rely, in
    preparing our financial statements prove inaccurate, our actual
    results may vary from those reflected in our projections and
    accruals.
     26




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If we
    fail to design and maintain an effective system of internal
    controls, we may not be able to accurately report our financial
    results or prevent fraud. As a result, current and potential
    stockholders could lose confidence in our financial reporting,
    which could harm our business and the trading price of our
    common stock.
  Form 10-K
      Factors
    Related to Development, Clinical Testing and Regulatory Approval
    of Our Drug Candidates
  All of
    our drug candidates are in development. Our drug candidates
    remain subject to clinical testing and regulatory approval. If
    we are unable to develop our drug candidates, we will not be
    successful.
  ® ® ® ® ® ® ® ®
   27




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
    offer therapeutic or other improvements over existing drugs;
    be proven safe and effective in clinical trials;
    meet applicable regulatory standards;
    be capable of being produced in commercial quantities at
    acceptable costs; or
    be successfully commercialized.    If our
    clinical trials are not successful, we will not obtain
    regulatory approval for the commercial sale of our drug
    candidates.
         28




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
    discussions with the FDA or comparable foreign authorities
    regarding the scope or design of our clinical trials;
    delays in obtaining, or the inability to obtain, required
    approvals from, or suspensions or termination by, institutional
    review boards or other governing entities at clinical sites
    selected for participation in our clinical trials;
    delays enrolling participants into clinical trials;
    lower than anticipated retention of participants in clinical
    trials;
    insufficient supply or deficient quality of drug candidate
    materials or other materials necessary to conduct our clinical
    trials;
    serious or unexpected drug-related side effects experienced by
    participants in our clinical trials; or
    negative results of clinical trials.    
    we may be unable to commence human clinical trials of any HCV
    drug candidates or other drug candidates;
    if the GSK license agreement with GSK is consummated, GSK may be
    unable to continue human clinical trials of IDX899 or commence
    human clinical trials of any other licensed compound;
    Novartis may choose not to license our drug candidates and we
    may not be able to enter into other collaborative arrangements
    for any of our other drug candidates; or
    we may not have the financial resources to continue the research
    and development of our drug candidates.  If our
    drug candidates fail to obtain U.S. and/or foreign regulatory
    approval, we and our partners will be unable to commercialize
    our drug candidates.
       29




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Our
    products will be subject to ongoing regulatory review even after
    approval to market such products is obtained. If we or our
    partners fail to comply with applicable U.S. and foreign
    regulations, we or our partners could lose approvals we or our
    partners have been granted and our business would be seriously
    harmed.
      If we
    or our partners fail to comply with ongoing regulatory
    requirements after receipt of approval to commercialize a
    product, we or our partners may be subject to significant
    sanctions imposed by the FDA, EMEA or other U.S. and foreign
    regulatory authorities.
    
    warning letters and other regulatory authority communications
    objecting to matters such as promotional materials and requiring
    corrective action such as revised communications to healthcare
    practitioners;
    civil penalties;
    criminal penalties;
    injunctions; 30




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
    product seizure or detention;
    product recalls;
    total or partial suspension of manufacturing; and
    FDA refusal to review or approve pending new drug applications
    or supplements to new drug applications for previously approved
    products,
    and/or
    similar rejections of marketing applications or supplements by
    foreign regulatory authorities.    If we
    do not comply with laws regulating the protection of the
    environment and health and human safety, our business could be
    adversely affected.
    Factors
    Related to Our Relationship with Novartis
  Novartis
    has substantial control over us and could delay or prevent a
    change in corporate control.
    
    the election of directors;
    any amendment of our restated certificate of incorporation or
    amended and restated by-laws;
    the approval of mergers and other significant corporate
    transactions, including a sale of substantially all of our
    assets; or
    the defeat of any non-negotiated takeover attempt that might
    otherwise benefit our other stockholders.    Novartis
    has the right to exercise control over certain corporate actions
    that may not otherwise require stockholder approval as long as
    it holds at least 19.4% of our voting stock.
    
    the authorization or issuance of additional shares of our
    capital stock or the capital stock of our subsidiaries, except
    for a limited number of specified issuances; 31




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
    any change or modification to the structure of our board of
    directors or a similar governing body of any of our subsidiaries;
    any amendment or modification to any of our organizational
    documents or those of our subsidiaries;
    the adoption of a three-year strategic plan;
    the adoption of an annual operating plan and budget, if there is
    no approved strategic plan;
    any decision that would result in a variance of total annual
    expenditures, capital or expense, in excess of 20% from the
    approved three-year strategic plan;
    any decision that would result in a variance in excess of the
    greater of $10.0 million or 20% of our profit or loss
    target in the strategic plan or annual operating plan;
    the acquisition of stock or assets of another entity that
    exceeds 10% of our consolidated net revenue, net income or net
    assets;
    the sale, lease, license or other disposition of any assets or
    business which exceeds 10% of our net revenue, net income or net
    assets;
    the incurrence of any indebtedness by us or our subsidiaries for
    borrowed money in excess of $2.0 million;
    any material change in the nature of our business or that of any
    of our subsidiaries;
    any change in control of Idenix or any subsidiary; and
    any dissolution or liquidation of Idenix or any subsidiary, or
    the commencement by us or any subsidiary of any action under
    applicable bankruptcy, insolvency, reorganization or liquidation
    laws.         32




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
    securities issued in connection with our acquisition of all of
    the capital stock or all or substantially all of the assets of
    another entity; and
    shares of common stock issued upon exercise of stock options or
    stock awards pursuant to compensation and equity incentive
    plans. Notwithstanding the foregoing, voting stock includes up
    to 1,399,106 shares that were reserved as of May 8,
    2003 for issuance under our 1998 equity incentive plan.    We
    currently depend on Novartis for substantially all our revenues
    and for the commercialization of
    Tyzeka®/Sebivo®

    and for support in the development of drug candidates Novartis
    has licensed from us. If our development, license and
    commercialization agreement with Novartis terminates, our
    business and, in particular, the development of our drug
    candidates and the commercialization of any products that we
    successfully develop could be harmed.
  ® ®
  ® ® ® ® ® ® ® ®
     33




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Novartis
    has the option to license from us drug candidates we discover,
    or in some cases, acquire. If Novartis does not exercise its
    option with respect to a drug candidate, our development,
    manufacture and/or commercialization of such drug candidate may
    be substantially delayed or limited.
  ® ®
  and/or
  If we
    breach any of the numerous representations and warranties we
    made to Novartis under the development and commercialization
    agreement or the stock purchase agreement, Novartis has the
    right to seek indemnification from us for damages it suffers as
    result of such breach. These amounts could be
    substantial.
      ® ®
 34




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If we
    materially breach our obligations or covenants arising under the
    development and commercialization agreement with Novartis, we
    may lose our rights to develop or commercialize our drug
    candidates.
  and/or
  If we
    issue capital stock, in certain situations Novartis will be able
    to purchase shares at par value to maintain its percentage
    ownership in Idenix and, if that occurs, this could cause
    dilution. In addition, Novartis has the right, under specified
    circumstances, to purchase a pro rata portion of other shares
    that we may issue.
  24-month
  
    the date that Novartis and its affiliates own less than 19.4% of
    our voting stock; or
    the date that Novartis becomes obligated under the stock
    purchase agreement to make the additional future contingent
    payments of $357.0 million to our stockholders who sold
    shares to Novartis in May 2003.    
    securities issuable in connection with any stock split, reverse
    stock split, stock dividend or recapitalization that we
    undertake that affects all holders of our common stock
    proportionately;
    shares that Novartis has the right to purchase at par value, as
    described above;
    shares of common stock issuable upon exercise of stock options
    and other awards pursuant to our 1998 Equity Incentive
    Plan; and 35




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
    securities issuable in connection with our acquisition of all
    the capital stock or all or substantially all of the assets of
    another entity.    If
    Novartis terminates or fails to perform its obligations under
    the development and commercialization agreement, we may not be
    able to successfully commercialize our drug candidates licensed
    to Novartis and the development and commercialization of our
    other drug candidates could be delayed, curtailed or
    terminated.
  ® ®
    Novartis
    has the right to market and sell products that compete with the
    drug candidates and products that we license to it, and any
    competition by Novartis could have a material adverse effect on
    our business.
    Factors
    Related to Our Dependence on Third Parties
  If we
    seek to enter into collaboration agreements for any drug
    candidates other than those licensed to Novartis and GSK and we
    are not successful in establishing such collaborations, we may
    not be able to continue development of those drug
    candidates.
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and/or
  
    we may be required to expend our own funds to advance the drug
    candidate to commercialization;
    revenue from product sales could be delayed; or
    we may elect not to develop or commercialize the drug candidate.  Our
    license agreement with GSK is important to our business. The
    royalties and other payments we receive under our licensing
    arrangement with GSK could be delayed, reduced or terminated if
    GSK terminates or fails to perform its obligations under its
    agreement with us or if GSK is unsuccessful in its sales
    efforts.
    and/or
  Our
    collaborations with outside scientists may be subject to
    restriction and change.
    We
    have depended on third-party manufacturers to manufacture
    products for us. If in the future we manufacture any of our
    products, we will be required to incur significant costs and
    devote significant efforts to establish these
    capabilities.
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and/or
  Factors
    Related to Patents and Licenses
  If we
    are unable to adequately protect our patents and licenses
    related to our drug candidates, or if we infringe the rights of
    others, it may not be possible to successfully commercialize
    products that we develop.
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® ®
      ® ®
     39




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
    ownership of patents and patent applications;
    the patentability of our inventions relating to our products and
    drug candidates; and/or
    the enforceability, validity or scope of protection offered by
    our patents relating to our products and drug candidates.          
    incur substantial monetary damages;
    encounter significant delays in bringing our drug candidates to
    market; and/or
    be precluded from participating in the manufacture, use or sale
    of our drug candidates or methods of treatment requiring
    licenses.  Confidentiality
    agreements with employees and others may not adequately prevent
    disclosure of trade secrets and other proprietary
    information.
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If any
    of our agreements that grant us the exclusive right to make, use
    and sell our drug candidates are terminated, we and/or
    collaboration partners may be unable to develop or commercialize
    our drug candidates.
  ® ® ® ®
     41




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If our
    cooperative research agreement with the University of Cagliari
    is terminated for breach, we may be unable to utilize research
    results arising out of that work prior to the
    termination.
    Factors
    Related to Our Common Stock
  Sales
    of additional shares of our common stock could result in
    dilution to existing stockholders and cause the price of our
    common stock to decline.
      Fluctuation
    of our quarterly results may cause our stock price to decline,
    resulting in losses to you.
    
    realization of license fees and achievement of milestones under
    our development and commercialization agreement with Novartis;
    realization of license fees and achievement of preclinical and
    clinical milestones and sales thresholds under the GSK license
    agreement;
    reductions in proceeds associated with Novartis right to
    maintain its percentage ownership of our voting stock when we
    issue shares at a price below fair market value;
    adverse developments regarding the safety and efficacy of
    Tyzeka®/Sebivo®

    or our drug candidates;
    the results of ongoing and planned clinical trials of our drug
    candidates, including the ongoing phase I/II, double-blind,
    placebo-controlled, dose-escalation study to evaluate the safety
    and antiviral activity of IDX184 in treatment-naïve adult
    patients infected with HCV;
    developments in the market with respect to competing products or
    more generally the treatment of HBV, HCV or HIV;
    the results of regulatory reviews relating to the approval of
    our drug candidates;
    the timing and success of the launch of products, if any, we
    successfully develop;
    future royalty payments received by us associated with sales of
    Tyzeka®/Sebivo®;
    the initiation or conclusion of litigation to enforce or defend
    any of our assets; and 42




---



##### Table of Contents




    general and industry-specific economic conditions that may
    affect our research and development expenditures.    An
    investment in our common stock may decline in value as a result
    of announcements of business developments by us or our
    competitors.
    
    our collaboration with Novartis;
    our collaboration with GSK;
    the results of our ongoing phase I/II, double-blind,
    placebo-controlled, dose-escalation study to evaluate the safety
    and antiviral activity of IDX184 in treatment-naïve adult
    patients infected with HCV;
    the results of discovery, preclinical studies and clinical
    trials by us or our competitors;
    the acquisition of technologies, drug candidates or products by
    us or our competitors;
    the development of new technologies, drug candidates or products
    by us or our competitors;
    regulatory actions with respect to our drug candidates or
    products or those of our competitors, including those relating
    to our clinical trials, marketing authorizations, pricing and
    reimbursement;
    the timing and success of launches of any product we
    successfully develop;
    future royalty payments received by us associated with sales of
    Tyzeka®/Sebivo®;
    the market acceptance of any products we successfully develop;
    significant changes to our existing business model;
    the initiation or conclusion of litigation to enforce or defend
    any of our assets; and
    significant acquisitions, strategic partnerships, joint ventures
    or capital commitments by us or our competitors.    We
    could be subject to class action litigation due to stock price
    volatility, which, if it occurs, will distract our management
    and could result in substantial costs or large judgments against
    us.
   43




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##### Table of Contents



Item 1B.Unresolved
    Staff Comments.    Item 2.
    Properties.    LeaseProperty Location

Approximate Square Feet


Use

Expiration DateCambridge, MA


49,912 sq ft


Office Headquarters


March 201039,014 sq ft


Office and Laboratory


December 2013Montpellier, France


35,215 sq ft


Office and Laboratory


April 2017     Item 3.
    Legal
    Proceedings.    Item 4.
    Submission
    of Matters to a Vote of Security Holders.   PART II  Item 5.
    Market
    for Registrants Common Equity, Related Stockholder Matters
    and Issuer Purchases of Equity Securities.  Market
    Information
    High


Low2008First quarter

$
5.59


$
2.57Second quarter

$
7.50


$
5.05Third quarter

$
10.10


$
6.52Fourth quarter

$
7.27


$
3.362007First quarter

$
10.83


$
7.18Second quarter

$
8.24


$
5.76Third quarter

$
6.07


$
2.29Fourth quarter

$
3.30


$
2.10   Stockholders
   44




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##### Table of Contents



Dividends
    Repurchase
    of Securities
    Item 6.
    Selected
    Consolidated Financial Data  Form 10-K. Form 10-K,
  Years Ended December 31,2008


2007


2006


2005


2004(In thousands, except per share data)Consolidated Statement of Operations Data:Total revenues

$
10,049


$
68,028


$
67,377


$
64,718


$
95,389Operating expensesCost of sales


1,745



2,001



62







Research and development


53,887



85,839



96,080



86,590



79,979Selling, general and administrative


27,130



63,348



56,954



33,657



23,603Restructuring and impairment charges


297



8,744











Total operating expenses


83,059



159,932



153,096



120,247



103,582Loss from operations


(73,010
)


(91,904
)


(85,719
)


(55,529
)


(8,193
)Investment and other income, net


781



6,387



9,487



4,038



1,383Gain on sale of equity securities






3,500











Income tax benefit (expense)


2,023



(498
)


1,145



714



566Net loss

$
(70,206
)

$
(82,515
)

$
(75,087
)

$
(50,777
)

$
(6,244
)Basic and diluted net loss per common share

$
(1.24
)

$
(1.47
)

$
(1.34
)

$
(1.03
)

$
(0.15
)Shares used in computing basic and diluted net loss per common
    share


56,403



56,169



56,005



49,395



41,369   As of December 31,2008


2007


2006


2005


2004(In thousands)Consolidated Balance Sheet Data:Cash and cash equivalents

$
41,509


$
48,260


$
55,892


$
83,733


$
42,083Working capital


30,465



72,985



110,159



167,069



70,123Total assets


79,780



160,540



228,465



277,657



187,118Deferred revenue


4,272



4,272



4,272



4,272



4,272Deferred revenue, related party, currrent


5,965



8,372



13,490



9,695



9,695Deferred revenue, related party, net of current portion


35,790



41,861



40,471



29,089



38,779Long-term obligations


12,789



14,835



2,251



2,792



3,691Accumulated deficit


(508,962
)


(438,756
)


(355,941
)


(280,854
)


(230,077
)Total stockholders equity


7,353



68,838



142,025



206,887



109,058  45




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##### Table of Contents



Item 7.
    Managements
    Discussion and Analysis of Financial Condition and Results of
    Operations  This report contains forward-looking statements
    within the meaning of Section 21E of the Securities
    Exchange Act of 1934, as amended, or the Exchange Act. For this
    purpose, any statements contained herein regarding our strategy,
    future operations, financial position, future revenues,
    projected costs and expenses, prospects, plans and objectives of
    management, other than statements of historical facts, are
    forward-looking statements. The words anticipate,
    believes, estimates,
    intends, may, plans,
    will, would and similar expressions are
    intended to identify forward-looking statements, although not
    all forward-looking statements contain these identifying words.
    Such statements reflect our current views with respect to future
    events. We cannot guarantee that we actually will achieve the
    plans, intentions, or expectations disclosed in our
    forward-looking statements. There are a number of important
    factors that could cause actual results or events to differ
    materially from those disclosed in the expressed or implied
    forward-looking statements we make. These important factors
    include our critical accounting policies and
    estimates and the risk factors set forth below in
    Part II, Item 1A  Risk Factors. Although we
    may elect to update forward-looking statements in the future, we
    specifically disclaim any obligation to do so, even if our
    estimates change, readers should not rely on those
    forward-looking statements as representing our views as of any
    date subsequent to the date of this Annual Report.
  Overview
  ® ®
  ® ®
  Indication

Product/Drug Candidates/Programs

DescriptionHBV

Tyzeka®/Sebivo®

    (telbivudine)
    (L- nucleoside)

Novartis has all development, commercialization and
    manufacturing rights and obligations related to telbivudine
    (Tyzeka®/Sebivo®)

    on a worldwide basis. We receive royalty payments equal to a
    percentage of net sales of
    Tyzeka®/Sebivo®.HIV

IDX899
    (non-nucleoside reverse transcriptase
    inhibitor or NNRTI)

In 2008, we successfully completed a proof-of-concept clinical
    study of IDX899 in treatment-naïve HIV infected patients.
    In February 2009, we granted GSK an exclusive license to
    develop, manufacture and commercialize IDX899. The GSK license
    agreement is subject to certain closing conditions.HCV

Discovery and development program

This program is focused on the three primary classes of drugs
    for the treatment of HCV, which include nucleoside/nucleotide
    polymerase inhibitors, protease inhibitors and non-nucleoside
    polymerase inhibitors. 46




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##### Table of Contents



Indication

Product/Drug Candidates/Programs

DescriptionIDX184 and IDX102
    (nucleotide polymerase inhibitors)

The most advanced of these efforts is our research on the
    next-generation nucleoside/nucleotide polymerase inhibitors. We
    successfully completed a phase I study in October 2008 and are
    currently evaluating IDX184 in a proof-of-concept clinical study
    in treatment-naive HCV-genotype-1-infected patients.
    Additionally, we have submitted several CTAs in Europe for
    IDX184.IDX102 is in late-stage preclinical development.IDX136 and IDX316
    (protease inhibitors)

We have selected IDX136 and IDX316 as our lead clinical
    candidates from this program and are conducting IND-enabling
    pharmacology and toxicology studies. We plan to submit an IND in
    the United States and a CTA in Europe for a protease inhibitor
    drug candidate in 2009, assuming positive results from the
    IND-enabling preclinical studies.IDX375
    (non-nucleoside polymerase inhibitor)

We have selected IDX375 as our lead clinical candidate from our
    non-nucleoside HCV polymerase inhibitor program. We are
    continuing IND-enabling pharmacology and toxicology studies and
    plan to submit an IND in the United States and a CTA in Europe
    for this drug candidate in 2009, assuming positive results from
    these studies.   project-by-project project-by-project
     47




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##### Table of Contents



Disease

Product/Drug

Years Ended December 31,Indication

Candidate

2006


2007


2008(In thousands)HBV


Tyzeka®/Sebivo®

$
36,310


$
24,147


$
265HBV


Valtorcitabine


3,726



1,515



21HCV


Valopicitabine


11,489



6,196



87HCV


IDX184 and IDX102






3,984



7,004HCV


Preclinical discovery program






243



7,222HIV


IDX899


5,817



8,824



3,978$
57,342


$
44,909


$
18,577   ® ®
  Novartis
    Collaboration
    ® ® ® ® ® ® ® ®
   48




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##### Table of Contents



® ® ® ®
  GSK
    Collaboration
    
    a license agreement whereby we granted GSK an exclusive license
    to develop, manufacture and commercialize our NNRTI compounds,
    including IDX899, for the treatment of human diseases, including
    HIV/AIDS, on a worldwide basis; and
    a stock purchase agreement, which we refer to as the GSK stock
    purchase agreement, under which GSK will purchase
    2,475,728 shares of our common stock at an aggregate
    purchase price of $17.0 million, or a per share price of
    $6.87.       49




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##### Table of Contents




    by mutual written agreement of the parties;
    by either party if a closing does not occur within 90 days
    following the filings made in connection with the HSR
    clearance; or
    by either us or GSK in the event that a governmental entity
    issues a final and nonappealable order, decree or injunction or
    takes any action to restrain, enjoin or prohibit the
    transactions contemplated by the GSK stock purchase agreement.            
    consented to the sale by us of the 2,475,728 shares to GSK;
    approved entering into the GSK license agreement;
    waived its rights to buy a pro rata portion of the shares issued
    to GSK;
    approved our granting of registration rights to GSK and waived
    its rights to participate in such registration; and
    waived, until a certain time, its rights to request that we file
    a registration statement on Novartis behalf or include
    shares of our common stock owned by Novartis in any such
    registration statement filed on behalf of GSK. 50




---



##### Table of Contents



Results
    of Operations
  Comparison
    of Years Ended December 31, 2008 and 2007
  Revenues
    Years Ended December 31,2008


2007(In thousands)Collaboration revenue  related party:Reimbursement of research and development costs

$
1,369


$
41,933License fee


5,561



13,535Royalty revenue


2,885



617Milestone revenue






10,000Product revenue  rest of world






46Profit sharing to related party






(1,380
)9,815



64,751Product sales, net


29



3,187Government grants


205



90Total revenues

$
10,049


$
68,028  51




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##### Table of Contents




    reimbursement by Novartis for expenses we incur in connection
    with the development and registration of our licensed products
    and drug candidates, net of certain qualifying costs incurred by
    Novartis;
    license and other fees received from Novartis for the license of
    HBV and HCV drug candidates, net of reductions for Novartis
    stock subscription rights, which is being recognized over the
    development period of the licensed drug candidates;
    milestone amounts from Novartis upon achievement of regulatory
    filings, certain marketing authorization approvals and other
    milestone payments; and
    royalty payments associated with product sales of
    Tyzeka®/Sebivo®

    made by Novartis.    
    product revenue  rest of world which is comprised of
    amounts that Novartis would pay us for the supply of licensed
    products in countries other than the following: the United
    States, United Kingdom, Germany, France, Spain and Italy. These
    amounts were recorded as revenue at a percentage of net
    sales; and
    profit sharing to related party which represents the net benefit
    amount paid to Novartis on licensed product sales in the United
    States in which we acted as the lead commercialization party.
    The net benefit, defined as net sales less cost of goods sold,
    was shared equally with Novartis on product sales in the United
    States. These amounts due to Novartis were recorded as a
    reduction of collaboration revenue.    ® ® ® ®
  Cost
    of Sales
    Research
    and Development Expenses
   52




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##### Table of Contents



Selling,
    General and Administrative Expenses
  ® ®
    Restructuring
    and Impairment Charges
    Investment
    and Other Income, Net
    Gain
    on Sale of Equity Securities
    Income
    Taxes
   53




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##### Table of Contents



Results
    of Operations
  Comparison
    of Years Ended December 31, 2007 and 2006
  Revenues
    Years Ended December 31,2007


2006(In thousands)Collaboration revenue  related partyReimbursement of research and development costs

$
41,933


$
54,858License fee revenue


13,535



12,049Royalty revenue


617



Milestone revenue


10,000



Product revenue  rest of world


46



Profit-sharing to related party


(1,380
)


(183
)64,751



66,724Product sales, net


3,187



424Government grants


90



229Total revenues

$
68,028


$
67,377     
    reimbursement by Novartis for expenses we incur in connection
    with the development and registration of our licensed products
    and drug candidates, net of certain qualifying costs incurred by
    Novartis;
    license and other fees received from Novartis for the license of
    HBV and HCV drug candidates, net of reductions for Novartis
    stock subscription rights, which is being recognized over the
    development period of the licensed drug candidates;
    milestone amounts from Novartis upon achievement of regulatory
    filings, certain marketing authorization approvals and other
    milestone payments; and
    royalty payments associated with product sales of
    Tyzeka®/Sebivo®

    made by Novartis.    
    product revenue  rest of world which is comprised of
    amounts that Novartis would pay us for the supply of licensed
    products in countries other than the following: the United
    States, United Kingdom, Germany, France, Spain and Italy. These
    amounts were recorded as revenue at a percentage of net
    sales; and
    profit sharing to related party which represents the net benefit
    amount paid to Novartis on licensed product sales in the United
    States in which we acted as the lead commercialization party.
    The net benefit, defined as net sales less cost of goods sold,
    was shared equally with Novartis on product sales in the United
    States. These amounts due to Novartis were recorded as a
    reduction of collaboration revenue.  ® ® ®
 54




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##### Table of Contents



® ® ®
  ®
  Cost
    of Sales
    Research
    and Development Expenses
  ® ® ®
  Selling,
    General and Administrative Expenses
  ® ®
  Restructuring
    and Impairment Charges
  ® ®
  Investment
    and Other Income, Net
    Gain
    on Sale of Equity Securities
   55




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##### Table of Contents



Income
    Taxes
  Accounting for
    Uncertain Tax Positions.
  Liquidity
    and Capital Resources
    
    license, milestone, royalty and other payments from Novartis;
    reimbursements from Novartis for costs we have incurred
    subsequent to May 8, 2003 in connection with the
    development of
    Tyzeka®/Sebivo®,

    valtorcitabine and valopicitabine;
    collections on sales of
    Tyzeka®

    in the United States through September 30, 2007;
    net proceeds from Sumitomo for reimbursement of development
    costs;
    net proceeds from private placements of our convertible
    preferred stock;
    net proceeds from public offerings;
    net proceeds from concurrent private placements of our common
    stock in July 2004 and in October 2005; and
    proceeds from the exercise of stock options granted pursuant to
    our equity compensation plans.  ® ®
     56




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##### Table of Contents



® ® ® ®
      Contractual
    Obligations and Commitments
    Payments Due by PeriodLess Than








After 5Contractual Obligations

Total


1 Year


1-3 Years


4-5 Years


Years(In thousands)Operating leases

$
14,352


$
3,399


$
4,601


$
4,061


$
2,291Consulting and other agreements


1,801



1,282



519







Long-term obligations


10,749







1,186



2,000



7,563Total contractual obligations

$
26,902


$
4,681


$
6,306


$
6,061


$
9,854          57




---



##### Table of Contents



® ®
           58




---



##### Table of Contents



Off-Balance
    Sheet Transactions
    Critical
    Accounting Policies and Estimates
    Form 10-K
  Revenue
    Recognition
  Revenue Recognition in
    Financial Statements,
  Collaboration Revenue  and/or No. 00-21, Accounting for Revenue Arrangements with Multiple
    Deliverables, No. 00-21. No. 00-21
     59




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##### Table of Contents



Collaboration Revenue  Related
    Party  Revenue Recognition,
      ® ® ® ®
 60




---



##### Table of Contents



Deferred Revenue 
  Valuation
    and Impairment of Investments and/or Marketable
    Securities
  Fair
    Value Measurements,
  
    Level 1  Observable inputs such as quoted prices
    in active markets;
    Level 2  Inputs, other than the quoted prices in
    active markets, that are observable either directly or
    indirectly; and
    Level 3  Unobservable inputs in which there is
    little or no market data, which requires the reporting entity to
    develop its own assumptions.      Accrued
    Expenses
   61




---



##### Table of Contents



Stock-Based
    Compensation
  Share-Based Payment
    No. 96-18, Accounting for Equity Instruments that Are Issued to Other
    than Employees for Acquiring, or in Conjunction with Selling,
    Goods or Services, EITF 96-18. EITF 96-18
     62




---



##### Table of Contents



Recent
    Accounting Pronouncements
  No. 157-3, Determining Fair Value of a Financial Asset in a Market That
    Is Not Active No. 157-3). No. 157-3 No. 157-3
  No. 157-2, Effective Date of FASB Statement No. 157, No. 157-2) No. 157-2
  No. 07-01, Accounting for Collaborative Arrangements Related to the
    Development and Commercialization of Intellectual Property, (EITF 07-01) EITF 07-01 EITF 07-01
  Item 7A.
    Quantitative
    and Qualitative Disclosure about Market Risk.  Interest
    Rate Risk
      Foreign
    Currency Exchange Rate Risk
  ®
  Item 8.
    Financial
    Statements and Supplementary Data.  Form 10-K.
  Item 9.
    Changes
    in and Disagreements With Accountants on Accounting and
    Financial Disclosure.   63




---



##### Table of Contents



Item 9A.
    Controls
    and Procedures.  Disclosure
    Controls and Procedures
  Evaluation
    of Disclosure Controls and Procedures.
  Rules 13a-15(e) 15d-15(e)
  Managements
    Annual Report on Internal Control Over Financial
    Reporting
  Rules 13a-15(f) 15d-15(f)
  
    pertain to the maintenance of records that in reasonable detail
    accurately and fairly reflect the transactions and dispositions
    of Idenixs assets;
    provide reasonable assurance that transactions are recorded as
    necessary to permit preparation of financial statements in
    accordance with GAAP, and that receipts and expenditures of
    Idenix are being made only in accordance with authorizations of
    our management and directors; and
    provide reasonable assurance regarding prevention or timely
    detection of unauthorized acquisition, use or disposition of
    Idenixs assets that could have a material effect on the
    financial statements.    Internal Control-Integrated
    Framework.
     64




---



##### Table of Contents



Changes
    in Internal Control Over Financial Reporting
  Rules 13a-15(f) 15d-15(f)
  Item 9B.
    Other
    Information.   65




---



##### Table of Contents



Part III  Form 10-K Form 10-K,
  Item 10.
    Directors,
    Executive Officers and Corporate Governance    Codes of
    Business Conduct
    Item 11.
    Executive
    Compensation      Item 12.
    Security
    Ownership of Certain Beneficial Owners and Management and
    Related Stockholder Matters    Item 13.
    Certain
    Relationships, Related Transactions and Director
    Independence    Item 14.
    Principal
    Accountant Fees and Services   66




---



##### 



PART IV  Item 15.
    Exhibits
    and Financial Statement Schedules  a)(1) Financial Statements: Form 10-K
   
 PageReport of Independent Registered Public
    Accounting Firm


68Consolidated Balance Sheets at December 31,
    2008 and 2007


69Consolidated Statements of Operations for the
    Years Ended December 31, 2008, 2007 and 2006


70Consolidated Statements of Stockholders
    Equity and Comprehensive Loss for the Years Ended
    December 31, 2008, 2007 and 2006


71Consolidated Statements of Cash Flows for the
    Years Ended December 31, 2008, 2007 and 2006


72Notes to the Consolidated Financial Statements


73    (a)(2) Financial Statement Schedules.
  (a)(3) Exhibits. Form 10-K
 67




---



##### Table of Contents



Report of
    Independent Registered Public Accounting Firm    Internal Control  Integrated
    Framework
        PricewaterhouseCoopers
    LLP
    68




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    BALANCE SHEETS
  December 31,2008


2007(In thousands,except share data)ASSETSCurrent assets:Cash and cash equivalents

$
41,509


$
48,260Restricted cash


411



411Marketable securities


1,424



39,862Receivables from related party


894



11,196Income taxes receivable


3,526



224Prepaid expenses and other current assets


2,277



3,766Total current assets


50,041



103,719Intangible asset, net


12,387



13,548Property and equipment, net


13,238



15,460Restricted cash, non-current


750



750Marketable securities, non-current


3,145



23,882Other assets


219



3,181Total assets

$
79,780


$
160,540LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable

$
3,868


$
5,372Accrued expenses


9,268



16,437Deferred revenue, related party


5,965



8,372Other current liabilities


475



553Total current liabilities


19,576



30,734Long-term obligations


12,789



14,835Deferred revenue


4,272



4,272Deferred revenue, related party, net of current portion


35,790



41,861Total liabilities


72,427



91,702Commitments and contingencies (Note 12 and 18)Stockholders equity:Common stock, $0.001 par value; 125,000,000 shares
    authorized at December 31, 2008 and 2007; 56,538,859 and
    56,189,467 shares issued and outstanding at
    December 31, 2008 and 2007, respectively


57



56Additional paid-in capital


515,883



506,800Accumulated other comprehensive income


375



738Accumulated deficit


(508,962
)


(438,756
)Total stockholders equity


7,353



68,838Total liabilities and stockholders equity

$
79,780


$
160,540    69




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF OPERATIONS
  Years Ended December 31,2008


2007


2006(In thousands, except per share data)Revenues:Collaboration revenue  related party

$
9,815


$
64,751


$
66,724Other revenue


234



3,277



653Total revenues


10,049



68,028



67,377Operating expenses:Cost of sales


1,745



2,001



62Research and development


53,887



85,839



96,080Selling, general and administrative


27,130



63,348



56,954Restructuring and impairment charges


297



8,744



Total operating expenses


83,059



159,932



153,096Loss from operations


(73,010
)


(91,904
)


(85,719
)Investment and other income, net


781



6,387



9,487Gain on sale of equity securities






3,500



Loss before income taxes


(72,229
)


(82,017
)


(76,232
)Income tax benefit (expense)


2,023



(498
)


1,145Net loss

$
(70,206
)

$
(82,515
)

$
(75,087
)Basic and diluted net loss per common share

$
(1.24
)

$
(1.47
)

$
(1.34
)Shares used in computing basic and diluted net loss per common
    share


56,403



56,169



56,005    70




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF STOCKHOLDERS EQUITY AND COMPREHENSIVE
    LOSS
 For the
    Years Ended December 31, 2008, 2007, 2006
  AccumulatedAdditional





Other





TotalCommon Stock


Paid-in


Deferred


Comprehensive


Accumulated


Stockholders


ComprehensiveShares


Amount


Capital


Compensation


Income (Loss)


Deficit


Equity


Loss(In thousands, except share data)Balance at December 31, 2005


55,813,275


$
56


$
488,340


$
(320
)

$
(335
)

$
(280,854
)

$
206,887Issuance of common stock upon exercise of stock options


260,612







892















892



Issuance of common stock upon vesting of stock options


14,442







44















44



Issuance of common stock with related party


3,303







54















54



Stock-based compensation for non-employees










30















30



Stock-based compensation










8,393



214











8,607



Antidilution shares contingently issuable to related party










25















25



Net loss






















(75,087
)


(75,087
)

$
(75,087
)Net change in unrealized holding gains on marketable securities


















191







191



191Cumulative translation adjustment


















382







382



382Comprehensive loss





























$
(74,514
)Balance at December 31, 2006


56,091,632


$
56


$
497,778


$
(106
)

$
238


$
(355,941
)

$
142,025Issuance of common stock upon exercise of stock options


97,835







205















205



Stock-based compensation










8,625



106











8,731



Antidilution shares contingently issuable to related party










192















192



Cumulative effect adjustment from adoption of FIN 48






















(300
)


(300
)


Net loss






















(82,515
)


(82,515
)

$
(82,515
)Net change in unrealized holding loss on marketable securities,
    net of tax


















(62
)






(62
)


(62
)Cumulative translation adjustment


















562







562



562Comprehensive loss





























$
(82,015
)Balance at December 31, 2007


56,189,467


$
56


$
506,800


$



$
738


$
(438,756
)

$
68,838Issuance of common stock upon exercise of stock options


339,067



1



729















730



Issuance of common stock with related party


10,325







35















35



Stock-based compensation










5,402















5,402



Antidilution shares contingently issuable to related party










2,917















2,917



Net loss






















(70,206
)


(70,206
)

$
(70,206
)Net change in unrealized holding gain on marketable securities,
    net of tax


















63







63



63Cumulative translation adjustment


















(426
)






(426
)


(426
)Comprehensive loss





























$
(70,569
)Balance at December 31, 2008


56,538,859


$
57


$
515,883


$



$
375


$
(508,962
)

$
7,353
     71




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  Years Ended December 31,2008


2007


2006(In thousands)Cash flows from operating activities:Net loss

$
(70,206
)

$
(82,515
)

$
(75,087
)Adjustments to reconcile net loss to net cash used in operating
    activities:Depreciation and amortization


5,403



8,955



3,463Stock-based compensation expense, including related to
    restructuring


5,402



8,731



8,637Revenue adjustment for contingently issuable shares


1,714



83



12Impairment charges






2,113



Gain on sale of equity securities






(3,500
)


Other


1,166



45



Changes in operating assets and liabilities:Receivables from related party


10,302



839



1,688Income taxes receivable


(287
)


(82
)


(1,347
)Prepaid expenses and other current assets


2,001



4,558



(2,981
)Other assets


(279
)


10



1,076Accounts payable


(1,502
)


(1,468
)


1,146Accrued expenses and other current liabilities


(7,173
)


(4,379
)


(60
)Deferred revenue, related party


(7,274
)


(3,618
)


15,189Other liabilities


(2,021
)


(451
)


(569
)Net cash used in operating activities


(62,754
)


(70,679
)


(48,833
)Cash flows from investing activities:Purchase of property and equipment


(2,250
)


(7,299
)


(9,561
)Purchases of marketable securities


(15,641
)


(92,702
)


(243,011
)Sales and maturities of marketable securities


73,211



159,017



272,496Proceeds from sale of equity securities of Pharmasset, Inc






4,000



Net cash provided by investing activities


55,320



63,016



19,924Cash flows from financing activities:Proceeds from exercise of common stock options


730



205



902Proceeds from issuance of common stock to related party


35







54Net cash provided by financing activities


765



205



956Effect of changes in exchange rates on cash and cash equivalents


(82
)


(174
)


112Net decrease in cash and cash equivalents


(6,751
)


(7,632
)


(27,841
)Cash and cash equivalents at beginning of year


48,260



55,892



83,733Cash and cash equivalents at end of year

$
41,509


$
48,260


$
55,892Supplemental disclosure of cash flow information:Taxes paid

$
132


$
196


$
144Supplemental disclosure of noncash investing and financing
    activities:Change in value of shares of common stock contingently issuable
    or issued to related party


2,917



192



25Accrued settlement amount






15,000



    72




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL STATEMENTS
  1.
    Organization
    and Business  ® ®
  Hart-Scott-Rodino
  ® ® ® ®
       73




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  ® ®
  2.
    Summary
    of Significant Accounting Policies    Principles
    of Consolidation
    Use of
    Estimates and Assumptions
    Cash
    and Cash Equivalents
      Concentration
    of Credit Risk
    ® ®
 74




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Marketable
    Securities
      Fair
    Value of Financial Instruments
    Fair Value Measurements, No. 157-2, Effective Date of FASB Statement No. 157,
    
    Level 1  Observable inputs such as quoted prices
    in active markets;
    Level 2  Inputs, other than the quoted prices in
    active markets, that are observable either directly or
    indirectly; and
    Level 3  Unobservable inputs in which there is
    little or no market data, which require the reporting entity to
    develop its own assumptions.   75




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    3-year
    OtherObservable


UnobservableInputs


Inputs(Level 2)


(Level 3)


Total(In thousands)Cash equivalents

$
19,993


$



$
19,993Marketable securities


2,834







2,834Auction rate securities






1,710



1,710$
22,827


$
1,710


$
24,537     Year EndedDecember 31, 2008Fair Value(In thousands)Beginning balance

$
11,050Purchases, sales, and settlements


(9,150
)Total realized losses


(190
)Ending balance

$
1,710   The Fair Value
    Option for Financial Assets and Financial Liabilities, Accounting for Certain Investments in
    Debt and Equity Securities,
 76




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Investment
    Intangible
    Asset
      Property
    and Equipment
    Impairment
    of Long-Lived Assets
  Accounting for the Impairment of Disposal of Long-Lived
    Assets
  construction-in-progress
 77




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Revenue
    Recognition
  Revenue Recognition in Financial Statements
  Collaboration Revenue  and/or No. 00-21, Accounting for Revenue Arrangements with Multiple
    Deliverable, No. 00-21). No. 00-21
        Collaboration Revenue  Related Party 
 78




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      ® ® ® ®
  ® ®
  Product Sales ® ® ® ®
    Government Grants
  Research
    and Development Expenses
    Patents
   79




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Share-Based
    Compensation
  Share-Based
    Payment
  No. 96-18, Accounting for Equity Instruments that Are Issued to Other
    than Employees for Acquiring, or in Conjunction with Selling,
    Goods or Services (EITF 96-18). EITF 96-18
  Foreign
    Currency
    Income
    Taxes
    Accounting for Uncertain Tax
    Positions
  Comprehensive
    Loss
   80




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Net
    Loss per Common Share
  Earnings Per Share
  Segment
    Reporting
  Disclosures About Segments of an
    Enterprise and Related Information,
  3.
    Novartis
    Relationship  Overview
      ® ® ® ® ® ®
  ® ® ®
 81




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  ®
    ® ®
    Stockholders
    Agreement
    Novartis
    Stock Purchase Rights
  24-month
 82




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
            Manufacturing
    and Packaging Agreements
  ® ®
 83




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  ® ®
  Product
    Sales Arrangements
  12-month 12-month
  ® ® ® ®
  ® ® ®
  4.
    Net Loss
    Per Common Share    Years Ended December 31,2008


2007


2006(In thousands, except per share data)Basic and diluted net loss per common share:Net loss

$
(70,206
)

$
(82,515
)

$
(75,087
)Basic and diluted weighted average number of common shares
    outstanding


56,403



56,169



56,005Basic and diluted net loss per common share

$
(1.24
)

$
(1.47
)

$
(1.34
)     Years Ended December 31,2008


2007


2006(In thousands)Options


5,678



5,712



4,387Contingently issuable shares to related party


1,871



790



77  84




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  5.
    Marketable
    Securities    December 31, 2008Gross Unrealized


Gross UnrealizedAmortized Cost


Gains


Losses


Market Value(In thousands)Type of security:Money market funds

$
19,993


$



$



$
19,993Corporate debt securities


2,665







(32
)


2,633U.S. government obligations


200



1







201Auction rate securities


1,710











1,710Accrued interest


42











42$
24,610


$
1


$
(32
)

$
24,579   December 31, 2007Gross Unrealized


Gross UnrealizedAmortized Cost


Gains


Losses


Market Value(In thousands)Type of security:Money market funds

$
21,702


$



$



$
21,702Commercial paper


1,993











1,993Corporate debt securities


56,361



15



(109
)


56,267Municipal bonds


1,990











1,990Auction rate securities


11,050











11,050Accrued interest


763











763$
93,859


$
15


$
(109
)

$
93,765   December 31,


December 31,2008


2007(In thousands)Contractual maturity:Maturing in one year or less

$
21,434


$
69,883Maturing after one year through two years


70



4,490Maturing after two years through ten years


1,158



7,274Maturing after ten years


1,917



12,118$
24,579


$
93,765   85




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  December 31,


December 31,2008


2007(In thousands)Classification in balance sheets:Cash equivalents

$
20,010


$
30,021Marketable securities


1,424



39,862Marketable securities, non-current


3,145



23,882$
24,579


$
93,765       3-year
    6.
    Receivables
    from Related Party    December 31,2008


2007(In thousands)Receivables from related party

$
894


$
11,196   ® ®
 86




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    7.
    Property
    and Equipment, Net    EstimatedUsefulLife

December 31,(Years)

2008


2007(In thousands)Scientific equipment

7

$
7,897


$
6,958Computer equipment and software

2


3,763



3,787Enterprise software

5


2,599



2,599Office furniture and equipment

5 - 7


1,539



1,642Leasehold improvements

*


11,522



11,043Construction-in-progress




64



6027,384



26,089Less  accumulated depreciation




(14,146
)


(10,629
)$
13,238


$
15,460     *
    
    Shorter of asset life or lease term.    construction-in-progress
  8.
    Accrued
    Expenses    December 31,2008


2007(In thousands)Research and development contract costs

$
785


$
2,050Payroll and benefits


4,407



4,231License fees


1,000



1,000Professional fees


455



1,309Short-term portion of accrued restructuring


138



1,838Short-term portion of accrued settlement payment


657



4,000Other


1,826



2,009$
9,268


$
16,437  87




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        9.
    Restructuring
    and Impairment Charges  ® ® ® ®
  Current








TotalLiability


Payments





Liabilityas of


and other


Additional


as ofDecember 31, 2007


Adjustments


Expense


December 31, 2008(In thousands)Employee severance, benefits and lease exit costs

$
1,838


$
(1,963
)

$
297


$
172     10.
    Common
    Stock        11.
    Equity
    Incentive Plans and Share-based Compensation   88




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
            Years Ended December 31,2008


2007


2006(In thousands)Research and development

$
2,005


$
3,005


$
2,892Selling, general and administrative


3,397



4,758



5,745Restructuring and impairment






968



Total stock-based compensation expense

$
5,402


$
8,731


$
8,637    89




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Years Ended December 31,2008


2007


2006Weighted-average fair value of options granted

$
2.99


$
2.83


$
8.38Risk-free interest rate


2.83
%


4.35
%


4.78
%Expected dividend yield


0
%


0
%


0
%Expected option term (in years)


5.1



5.1



5.0Expected volatility


63.2
%


59.5
%


63.0
%       Number


Weighted


Weighted Averageof Options


Average Exercise


Remaining


AggregateOutstanding


Price per Share


Contractual Term


Intrinsic Value(In thousands)Outstanding, December 31, 2007


5,708,264


$
9.83Granted


1,339,300



5.33Exercised


(339,067
)


2.15Cancelled


(1,030,509
)


13.03Outstanding, December 31, 2008


5,677,988


$
8.64



6.71


$
4,794Exercisable, December 31, 2008


3,220,501


$
10.72



5.36


$
1,890Vested and expected to vest, December 31, 2008


4,947,498


$
9.07



6.52


$
3,964         12.
    Commitments
    and Contingencies  Lease
    Arrangements
   90




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    OperatingYear Ending December 31,

Leases(In thousands)2009

$
3,3992010


2,4602011


2,1412012


2,0382013


2,0232014 and thereafter


2,291Total

$
14,352       48-month
    Legal
    Contingencies
  Hepatitis
    C Drug Candidates
   91




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
        Hepatitis
    B Product
  ® ®
   92




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Indemnification
   93




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  13.
    Income
    Taxes    2008


2007


2006(In thousands)Loss before income taxesU.S.

$
(73,521
)

$
(82,210
)

$
(61,877
)Foreign


1,292



193



(14,355
)$
(72,229
)

$
(82,017
)

$
(76,232
)Income tax (benefit) expenseCurrentFederal  U.S.

$



$
(257
)

$
(48
)State  U.S.


(49
)


176



135Foreign


(1,974
)


579



(1,232
)(2,023
)


498



(1,145
)DeferredFederal  U.S.

$



$



$
State  U.S.










Foreign


















Total income tax (benefit) expense

$
(2,023
)

$
498


$
(1,145
)      94




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2008


2007(In thousands)Depreciation

$
1,337


$
132Development contracts


1,609



1,909Nonqualified stock options


4,394



3,350Deferred licensing income


15,499



16,320Accrued expenses and other


2,516



3,586Capitalized research costs


23,246



28,842Research and development credits


7,629



5,555Foreign tax credit carryforward


877



1,326Net operating carryforwards


91,670



64,204Valuation allowance


(148,777
)


(125,224
)Deferred tax asset

$



$
     Accounting for Income
    Taxes,
      2008


2007


2006Federal statutory rate benefit


(34
)%


(34
)%


(34
)%Foreign tax expense (benefit)


(3
)






(1
)State tax benefit, net of federal benefit


1



(4
)


(10
)Permanent items


1



1



(35
)Foreign rate differentials










7Valuation allowance


32



38



72Effective income tax rate


(3
)%


1
%


(1
)%  95




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
          2008


2007Balance at January 1

$
2,840


$
7,934Additions based on tax positions related to the current period


642



459Additions for tax positions of prior periods


342



1,324Reductions for tax positions of prior periods


(410
)


(6,877
)Settlements






Balance at December 31

$
3,414


$
2,840          96




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      14.
    Employee
    Benefit Plans        15.
    Related
    Party Transactions  ® ®
  ®
  16.
    Segment
    Reporting    2008


2007(In thousands)United States

$
9,449


$
11,530Europe


3,789



3,930$
13,238


$
15,460   17.
    Licensing
    Agreements  UAB
    Research Foundation
   97




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      18.
    Collaborative
    Agreements and Contracts  CNRS
    and the University of Montpellier
    University
    of Cagliari
     98




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Sumitomo
    Pharmaceuticals Co., Ltd.
        Microbiologica
    Quimica E Farmaceutica Ltda
   99




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Metabasis
    Therapeutics, Inc.
      19.
    GlaxoSmithKline
    License Agreement    
    a license agreement whereby the Company granted GSK an exclusive
    license to develop, manufacture and commercialize its NNRTI
    compounds, including IDX899, for the treatment of human
    diseases, including HIV/AIDS, on a worldwide basis; and
    a stock purchase agreement under which GSK will purchase
    2,475,728 shares of the Companys common stock at an
    aggregate purchase price of $17.0 million, or a per share
    price of $6.87.     100




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
            
    consented to the sale by the Company of the
    2,475,728 shares to GSK;
    approved entering into the GSK License Agreement;
    waived its rights to buy a pro rata portion of the shares issued
    to GSK;
    approved the Companys granting of registration rights to
    GSK and waived its rights to participate in such
    registration; and
    waived, until a certain time, its rights to request that the
    Company files a registration statement on Novartis behalf
    or include shares of the Companys common stock owned by
    Novartis in any such registration statement filed on behalf of
    GSK.     101




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      20.
    Quarterly
    Financial Data (Unaudited)  First


Second


Third


Fourth


TotalQuarter


Quarter


Quarter


Quarter


Year(In thousands, except per share amounts)2008Total revenues

$
2,044


$
1,592


$
2,145


$
4,268


$
10,049Total operating expenses


23,844



21,239



19,846



18,130



83,059Net loss


(20,460
)


(18,906
)


(16,891
)


(13,949
)


(70,206
)Basic and diluted net loss per common share

$
(0.36
)

$
(0.34
)

$
(0.30
)

$
(0.25
)

$
(1.24
)2007Total revenues

$
24,806


$
19,732


$
10,888


$
12,602


$
68,028Total operating expenses


38,464



44,574



43,530



33,364



159,932Net loss


(11,569
)


(22,902
)


(30,549
)


(17,495
)


(82,515
)Basic and diluted net loss per common share

$
(0.21
)

$
(0.41
)

$
(0.54
)

$
(0.31
)

$
(1.47
)   21.
    Recent
    Accounting Pronouncements  No. 157-3, Determining Fair Value of a Financial Asset in a Market That
    Is Not Active No. 157-3). No. 157-3 No. 157-3
  No. 157-2, Effective Date of FASB Statement No. 157, No. 157-2) No. 157-2
 102




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  No. 07-01, Accounting for Collaborative Arrangements Related to the
    Development and Commercialization of Intellectual Property, (EITF 07-01) EITF 07-01 EITF 07-01
 103




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##### Table of Contents



SIGNATURES      /s/  Jean-Pierre
    Sommadossi   Chairman and Chief Executive Officer
      Name

Title

Date/s/  Jean-Pierre
    SommadossiJean-Pierre
    Sommadossi

Chairman, Chief Executive Officer and Director (Principal
    Executive Officer)

March 4, 2009/s/  Ronald
    C. Renaud, Jr.Ronald
    C. Renaud, Jr.

Chief Financial Officer and Treasurer 
    (Principal Financial and 
    Accounting Officer)

March 4, 2009/s/  Charles
    CrambCharles
    Cramb

Director

March 4, 2009/s/  Wayne
    HockmeyerWayne
    Hockmeyer

Director

March 4, 2009/s/  Thomas
    HodgsonThomas
    Hodgson

Director

March 4, 2009/s/  Robert
    PelzerRobert
    Pelzer

Director

March 4, 2009/s/  Denise
    Pollard-KnightDenise
    Pollard-Knight

Director

March 4, 2009/s/  Steven
    ProjanSteven
    Projan

Director

March 4, 2009/s/  Pamela
    Thomas-GrahamPamela
    Thomas-Graham

Director

March 4, 2009  104




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##### Table of Contents



EXHIBIT INDEX  Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

NumberArticles of Incorporation and By-Laws3.1

Restated Certificate of Incorporation of the Registrant

S-1


3
.1


12/15/2003



333-1111573.2

Certificate of Amendment of Restated Certificate of
    Incorporation

10-Q for 6/30/2004


3
.1


8/26/2004



000-498393.3

Certificate of Amendment of Restated Certificate of
    Incorporation

10-K for 12/31/2005


3
.3


3/16/2006



000-498393.4

Certificate of Amendment of Restated Certificate of Incorporation

10-K for 12/31/2007


3
.4


3/14/2008



000-498393.5

Amended and Restated By-Laws

10-Q for 6/30/2004


3
.2


8/26/2004



000-498394.1

Specimen Certificate evidencing the Common Stock, $.001 par
    value

S-1 Amendment 2


4
.1


1/27/2004



333-111157Material contracts  real estate10.1

Lease Agreement, dated as of October 15, 1998, by and
    between Idenix (Massachusetts) Inc. and CambridgePark One
    Limited Partnership, as amended by the First Amendment to Lease
    dated as of September 1, 2001

S-1


10
.2


12/15/2003



333-11115710.2

Lease Agreement, dated as of August 22, 2001, by and
    between Idenix (Massachusetts) Inc. and West Cambridge Sciences
    Park

S-1


10
.3


12/15/2003



333-11115710.3

Amended and Restated Lease of Premises at 60 Hampshire Street,
    Cambridge, Massachusetts, dated as of October 28, 2003, by
    and between Idenix (Massachusetts) Inc. and BHX, LLC, as trustee
    of 205 Broadway Realty Trust

S-1


10
.4


12/15/2003



333-11115710.4

Administrative Lease Hotel DEnterprises Cap Gamma dated
    April 18, 2005 by and among Idenix SARL, Societe
    DEquipment de la Region Montpellieraine and the Communate
    DAgglomeration de Montpellier (English Translation)

8-K


10
.1


4/20/2005



000-4983910.5+

Offer of Sale Hotel

8-K


10
.2


4/20/2005



000-4983910.6

Joint Guarantee made as of December 15, 2005 between the
    Registrant and Societe DEquipment de la Region
    Montpellieraine

8-K


10
.3


4/20/2005



000-4983910.7

Indenture of Lease, dated June 8, 2005, by and between the
    Registrant and One Kendall Square Associates LLC

8-K


10
.1


6/13/2005



000-4983910.8

First Amendment of Lease dated July 24, 2006 by and between
    the Registrant and RB Kendall Fee, LLC

10-Q for 6/30/2006


10
.3


8/8/2006



000-49839   105




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##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.9

Second Amendment of Lease dated September 7, 2006 by and
    between the Registrant and RB Kendall Fee, LLC

10-Q for
    9/30/2006


10
.1


11/8/2006



000-49839Material contracts Novartis10.10

Letter Agreement, dated as of March 21, 2003, by and
    between the Registrant and Novartis Pharma AG

S-1
    Amendment 3


10
.28


7/6/2004



333-11115710.11

Amendment No. 1 to Letter Agreement, dated on or about
    January 28, 2009, by and between the Registrant and
    Novartis Pharma AG

8-K


10
.3


2/6/2009



000-4983910.12+

Restated and Amended Cooperative Agreement dated as of
    May 8, 2003, by among Idenix SARL and Le Centre National de
    la Recherche Scientifique, LUniversite Montpellier II
    and Novartis Pharma AG

S-1


10
.14


12/15/2003



333-11115710.13+

Letter Agreement, dated May 8, 2003, by and among the
    Registrant, Idenix SARL, Novartis Pharma AG and the University
    of Cagliari, amending the Cooperative Agreement and License
    Agreement

S-1


10
.18


12/15/2003



333-11115710.14+

Development, License and Commercialization Agreement, dated as
    of May 8, 2003, by and among the Registrant, Idenix
    (Cayman) Limited and Novartis Pharma AG, as amended on
    April 30, 2004

S-1


10
.24


12/15/2003



333-11115710.15+

Master Manufacturing and Supply Agreement, dated as of
    May 8, 2003, by and between Idenix (Cayman) Limited and
    Novartis Pharma AG

S-1


10
.25


12/15/2003



333-111157 106




---



##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.16+

Second Amendment, dated as of December 21, 2004, to the
    Development, License and Commercialization Agreement, by and
    among the Registrant, Idenix (Cayman) Limited and Novartis
    Pharma AG, as amended on April 30, 2004

10-K for
    12/31/2004


10
.16


3/17/2005



000-4983910.17+

Amendment No. 3 to the Development, License and
    Commercialization Agreement, effective as of February 27,
    2006, by and among the Registrant, Idenix (Cayman) Limited and
    Novartis Pharma AG

10-K for
    12/31/2005


10
.14


3/16/2006



000-4983910.18+

Amendment No. 4 to the Development, License and
    Commercialization Agreement, dated as of September 28,
    2007, by and among the Registrant, Idenix (Cayman) Limited and
    Novartis Pharma AG

10-Q for
    9/30/2007


10
.1


11/8/2007



000-4983910.19

Amendment No. 5 to the Development License and
    Commercialization Agreement, dated on or about January 28,
    2009, between the Registrant, Idenix (Cayman) Limited and
    Novartis Pharma AG

8-K


10
.2


2/6/2009



000-4983910.20+

Transition Services Agreement, dated as of September 28,
    2007, by and among the Registrant, Idenix (Cayman) Limited and
    Novartis Pharma AG

10-Q for
    9/30/2007


10
.2


11/8/2007



000-4983910.21

Amended and Restated Stockholders Agreement, dated
    July 27, 2004, by and among the Registrant, Novartis and
    the stockholders identified on the signature pages thereto

10-K for 
    12/31/2004


10
.20


3/17/2005



000-4983910.22

Par Value Stock Purchase Agreement, dated July 27,
    2004, by and between the Registrant and Novartis Pharma AG

10-K for
    12/31/2004


10
.21


3/17/2005



000-4983910.23+

Stock Purchase Agreement, dated as of March 21, 2003, by
    and among the Registrant, Novartis and the stockholders
    identified on the signature pages

S-1
    Amendment 3


10
.27


7/6/2004



333-1111510.24

Concurrent Private Placement Stock Purchase Agreement, dated
    July 27, 2004, by and between the Registrant and Novartis
    Pharma AG

10-K for
    12/31/2004


10
.22


3/17/2005



000-4983910.25+

Commercial Manufacturing Agreement dated as of June 22,
    2006 by and between the Registrant and Novartis Pharma AG

10-Q for
    6/30/2006


10
.1


8/8/2006



000-49839 107




---



##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.26+

Packaging Agreement dated as of June 22, 2006 by and
    between the Registrant and Novartis Pharma AG

10-Q for
    6/30/2006


10
.2


8/8/2006



000-4983910.27

Stock Purchase Agreement, dated February 4, 2009, between
    the Registrant and SmithKline Beecham Corporate

8-K


10
.1


2/6/2009



000-4983910.28+

License Agreement, dated February 4, 2009, between the
    Registrant and SmithKline Beecham Corporate

*University of Cagliari10.29+

Cooperative Antiviral Research Activity Agreement (the
    Cooperative Agreement), dated January 4, 1999,
    by and between Idenix SARL and the University of Cagliari

S-1


10
.16


12/15/2003



333-11115710.30+

License Agreement, dated as of December 14, 2000, between
    the Registrant and the University of cagliari




10
.17


12/15/2003



333-11115710.31+

Letter Agreement, dated April 10, 2002, by and between
    Idenix SARL and the University of Cagliari, amending the
    Cooperative Agreement and License Agreement

S-1


10
.18


12/15/2003



333-11115710.32+

Agreement, dated June 30, 2004, by and among the
    Registrant, Idenix SARL and the University of Cagliari

S-1
    Amendment 3


10
.18.1


7/6/2004



333-11115710.33

Collaborative Activities

S-1


10
.18.2


7/6/2004



333-11115710.34+

Agreement, dated October 24, 2005, by and among the
    Registrant, Idenix SARL and the Universita degli Studi di
    Cagliari,

10-Q for
    9/30/2005


10
.1


11/08/2005



000-4983910.35+

Amendment Agreement, dated February 4, 2009, by and among
    the Registrant, Idenix SARL, SmithKline Beecham Corporate,
    Universita degli Studi di Cagliari and Paolo LaColla

*Miscellaneous10.36+

License Agreement dated as of June 20, 1998 by and between
    the Registrant and the UAB Research Foundation, as amended by
    that First Amendment Agreement, dated as of June 20, 1998,
    and by that Second Amendment Agreement, dated as of
    July 16, 1999

S-1
    Amendment 2


10
.31


1/27/2004



333-111157 108




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##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.37

Master Services Agreement, dated February 25, 2003, by and
    between the Registrant and Quintiles, Inc.

S-1


10
.20


12/15/2003



333-11115710.38+

Master Services Agreement, dated May 27, 1999, between
    Idenix (Massachusetts), Inc. and Quintiles Scotland Ltd

S-1


10
.21


12/15/2003



333-11115710.39+

License Agreement, dated as of June 20, 1998, by and among
    the Registrant, TherapX Pharmaceuticals, L.L.C. and Raymond
    Schinazi

S-1


10
.15


12/15/2003



333-11115710.40

Multiproject Development and Supply Agreement, dated as of
    December 20, 2001, by and among the Registrant, Idenix SARL
    and Clariant Life Science Molecules (Missouri) Inc.

S-1


10
.22


12/15/2003



333-11115710.41+

Agreement, dated as of May 1, 2003, between Idenix (Cayman
    Limited and Microbiologica Quimica E Farmaceutica Ltda.

S-1
    Amendment 3


10
.23


7/6/2004



333-11115710.42

Final Settlement Agreement, dated March 26, 2003, by and
    between the Registrant and Sumitomo Pharmaceuticals Co.,
    Ltd.

S-1


10
.13


12/15/2003



333-11115710.43

Settlement Agreement, dated as of May 28, 2004, by and
    between the Registrant, Jean-Pierre Sommadossi, the University
    of Alabama at Birmingham and the University of Alabama Research
    Foundation

S-1
    Amendment 2


10
.34


5/28/2004



333-11115710.44

Settlement Agreement, effective June 1, 2008, by and among
    the Registrant, Jean-Pierre Sommadossi, the University of
    Montpellier II, Le Centre National de la Recherche Scientifique,
    the Board of Trustees of the University of Alabama on behalf of
    the University of Alabama at Birmingham, the University of
    Alabama Research Foundation and Emory University

8-K


10
.1


8/5/2008



000-4983910.45

Master Service Agreement, dated April 1, 2008, by and
    between the Registrant and Parexel International LLC

10-Q for
    6/30/2008


10
.1


8/7/2008



000-4983910.46+

Agreement, dated December 3, 2008, by and between the
    Registrant and Paolo LaColla

*Material contracts  management contracts and
    compensatory plans 109




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##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.47#

Form of Incentive Stock Option Agreement for awards granted
    pursuant to the 2005 Stock Incentive Plan, as amended

8-K


10
.2


6/13/2005



000-4983910.48#

Form of Non-Statutory

8-K


10
.3


6/13/2005



000-4983910.49#

Form of Incentive Stock Option Agreement for awards granted
    pursuant to the 2004 Stock Incentive Plan

10-K for 12/31/2004


10
.28


3/17/2005



000-4983910.50#

Form of Non-Statutory Stock Option Agreement for awards granted
    pursuant to the 2004 Stock Incentive Plan

10-K for 12/31/2004


10
.29


3/17/2005



000-4983910.51#

2005 Stock Incentive Plan

8-K


10
.4


6/13/2005



000-4983910.52#

2004 Stock Incentive Plan

S-1
    Amendment 2


10
.32


5/28/2004



333-11115710.53#

Amended and Restated 1998 Equity Incentive Plan

S-1
    Amendment 2


10
.1


5/28/2004



333-11115710.54#

Employment Agreement, dated as of May 6, 2003, by and
    between the Registrant and Jean-Pierre Sommadossi

S-1


10
.5


12/15/2003



333-11115710.55#

Amendment No. 1 to Employment Agreement, dated
    December 23, 2008, between the Registrant and Jean-Pierre
    Sommadossi

*10.56#

Employment Letter, dated August 18, 2006, by and between
    the Registrant and John Weidenbruch

8-K


10
.1


9/8/2006



000-4983910.57#

Employment Letter, dated January 7, 2007, by and between
    the Registrant and Douglas L. Mayers, M.D.

8-K


10
.1


5/8/2007



000-4983910.58#

Employment Letter, dated June 13, 2007, by and between the
    Registrant and Ronald C. Renaud, Jr.

8-K


10
.1


6/19/2007



000-4983910.59#

Employment Letter, dated May 14, 2008, by and between the
    Registrant and David N. Standring, Ph.D

8-K


10
.1


5/15/2008



000-49839Additional Exhibits21.1

Subsidiaries of the Company

*23.1

Consent of PricewaterhouseCoopers LLP, an independent registered
    public accounting firm

*31.1

Certification of Chief Executive Officer pursuant to
    Rule 13a-14(a)/15d-14(a)
    of the Securities Exchange Act of 1934, as amended

*31.2

Certification of Chief

* 110




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##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number32.1

Certification of Chief Executive Officer pursuant to 18 U.S.C.
    §1350, as adopted pursuant to Section 906 of
    the                  Sarbanes-Oxley Act of 2002

*32.2

Certification of Chief Financial Officer pursuant to
    18 U.S.C. §1350, as adopted pursuant to Section 906 of
    the Sarbanes-Oxley Act of 2002

*     *
    
    File herewith#
    
    Management contract or compensatory plan or arrangement filed as
    an exhibit to this report pursuant to Items 15(a) and 15(c)
    of
    Form 10-K+
    
    Confidential treatment requested as to certain portions, which
    portions have been separately filed with the Securities and
    Exchange Commission 111