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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, 2007oro

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
    Incorporation or Organization)

(I.R.S. Employer
    Identification No.)60 Hampshire Street,
    Cambridge, Massachusetts(Address of Principal
    Executive Offices)

02139(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
  Rule 12b-2
  Large accelerated
    filer o

Accelerated
    filer þ

Non-accelerated
    filer o
    (Do not check if a smaller reporting company)

Smaller reporting
    company o   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


23Item 1B.


Unresolved Staff Comments


47Item 2.


Properties


47Item 3.


Legal Proceedings


47Item 4.


Submission of Matters to a Vote of Security
    Holders


48PART IIItem 5.


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


48Item 6.


Selected Consolidated Financial Data


49Item 7.


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


50Item 7A.


Quantitative and Qualitative Disclosure about
    Market Risk


68Item 8.


Financial Statements and Supplementary Data


68Item 9.


Changes in and Disagreements with Accountants on
    Accounting and Financial Disclosure


68Item 9A.


Controls and Procedures


69Item 9B.


Other Information


70PART IIIItem 10.


Directors, Executive Officers and Corporate
    Governance


71Item 11.


Executive Compensation


71Item 12.


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


71Item 13.


Certain Relationships, Related Transactions and
    Director Independence


71Item 14.


Principal Accountant Fees and Services


71PART IVItem 15.


Exhibits and Financial Statement Schedules


72SIGNATURES


108Exhibit Index


109Ex-3.4 Certificate of Amendment of Restated Certificate of IncorporationEx-21.1 Subsidiaries of the CompanyEx-23.1 Consent of PricewaterhouseCoopers LLPEx-31.1 Section 302 Certification of CEOEx-31.2 Section 302 Certification of CFOEx-32.1 Section 906 Certification of CEOEx-32.2 Section 906 Certification of CFO   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.  The
    Company
      2007
    Developments
  HBV
  ® ® ® ® ®
  ® ® ® ®
  ® ®
    HCV
      HIV
   4




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Overview
              Form 10-K. Form 10-K, Form 10-Q, Form 8-K www.sec.gov. 1-800-SEC-0330.
  617-995-9800.
 5




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Form 10-K
  ® ® ® ®
  Products
    and Product Candidates
    Hepatitis
    C
  HCV
    Discovery Program
    and/or
     6




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Valopicitabine
    HIV
  once-a-day
  7-day
  Hepatitis
    B
  Telbivudine
  Transition
    to Novartis
  ® ®
     7




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Phase
    IIIb/IV Clinical Trials
  ® ® ® ® ® ®
  Valtorcitabine
    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
 8




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Research
    and Development Expenses
    Collaborations
  Relationship
    with Novartis
  Overview
    
    the development and commercialization agreement, under which we
    collaborate with Novartis to develop, manufacture and
    commercialize our HBV product candidates and our HCV and other
    product 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 product 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 an
    HCV product candidate.    Development,
    License and Commercialization Agreement
  Designation
    of Products
    
    Tyzeka®/Sebivo®,
    which was transferred to Novartis pursuant to the 2007 Amendment;
    valtorcitabine, our HBV product candidate, which we no longer
    continue to develop; and
    valopicitabine, our HCV product candidate, which was placed on
    clinical hold by the FDA in July 2007 based on the overall
    risk/benefit profile observed in clinical testing.   9




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® ®
  ® ® ®
        Development
    of Products and Regulatory Activities
      Product
    Commercialization
  ® ® ® ®
 10




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Exclusivity
  country-by-country
  Indemnification
    Termination
    
    with respect to the particular product, product candidate or
    country to which the breach relates; or
    in its entirety, if the material breach is not limited to a
    particular product, product candidate or country.   11




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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;
    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; and
    required that, with certain limited exceptions, Novartis and its
    affiliates not acquire additional shares of our voting stock
    unless a majority of our independent directors approves or
    requests the acquisition. These restrictions will terminate on
    May 8, 2008, unless sooner terminated under the terms of
    the stockholders agreement.  Novartis
    Stock Purchase Rights
   12




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Stock
    Purchase Agreement
      Co-operative
    Laboratory Agreements
  CNRS
    and the University of Montpellier
    University
    of Cagliari
     13




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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.         15




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16




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® ®
  Hepatitis
    C Patent Portfolio
      HIV
    Patent Portfolio
      non-U.S. patent
  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. 17




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® ®
  ® ® ® 2-a
    Pharmaceutical
    Pricing and Reimbursement
     18




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Regulatory
    Matters
  ® ® ® ® ®
    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
 19




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30-day 30-day
            6-month
   20




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and/or and/or
  and/or
      Foreign
    Regulation of Drug Product Approval
    Europe
   21




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Mutual Recognition Procedure and Decentralized
    Approval.
    Centralized Procedure.
    Asia
    Marketing
    Applications Format
  e-CTDs,
 22




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Hazardous
    Materials
    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.
  ® ®
  We
    will need additional capital to fund our operations, including
    the development, manufacture and potential commercialization of
    our product candidates. If we do not have or cannot raise
    additional capital when needed, we will be unable to develop and
    ultimately commercialize our product candidates
    successfully.
   23




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® ®
    
    with respect to
    Tyzeka®/Sebivo®,
    the level of royalty payments received from Novartis is
    significant;
    with respect to our other product candidates, Novartis exercises
    its option to license other product candidates, and we receive
    related license fees, milestone payments and development expense
    reimbursement payments from Novartis; and with respect to our
    other product candidates not licensed by Novartis, we receive
    related license fees, milestone payments and development expense
    reimbursement payments from third parties.      
    the amount of revenue that we may be able to realize from
    commercialization and sale of product 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;
    the cost of obtaining, maintaining and defending patents on
    telbivudine, our product candidates and our processes;
    the cost, timing and outcome of regulatory reviews;
    the cost of re-establishing sales and marketing functions;
    the commercial potential of our product candidates;
    the rate of technological advances in our markets;
    the cost of acquiring or in-licensing new discovery compounds,
    technologies, product 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
     24




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Our
    research and development efforts may not result in additional
    product 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
    product 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.
  and/or
 25




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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 product candidates may be
    rendered noncompetitive or obsolete.
    ® ®
    
    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 product candidates that are
    in late-stage development; and
    collaborative arrangements in our target markets with leading
    companies and research institutions.    and/or
  ® ®
 26




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If we
    are not able to attract and retain key management and scientific
    personnel and advisors, we may not successfully develop our
    product candidates or achieve our other business
    objectives.
      Our
    business has a substantial risk of product liability claims. If
    we are unable to obtain 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.
   27




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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.
      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 Product Candidates
  All of
    our product candidates are in development. Our product
    candidates remain subject to clinical testing and regulatory
    approval. If we are unable to develop our product candidates, we
    will not be successful.
  ® ® ® ®
 28




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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 product
    candidates.
       29




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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 product 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 HIV
    product candidate, HCV product candidates or other product
    candidates;
    Novartis may choose not to license our product candidates and we
    may not be able to enter into other collaborative arrangements
    for any of our other product candidates; or
    we may not have the financial resources to continue the research
    and development of our product candidates.  If our
    product candidates fail to obtain U.S. and/or foreign regulatory
    approval, we and our partners will be unable to commercialize
    our product candidates.
     30




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Our
    products will be subject to ongoing regulatory review even after
    approval to market such products is obtained. If we fail to
    comply with applicable U.S. and foreign regulations, we could
    lose approvals we have been granted and our business would be
    seriously harmed.
      If we
    are subject to unfavorable pricing regulations, third-party
    reimbursement practices or healthcare reform initiatives, our
    business may be harmed.
   31




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If we
    fail to comply with ongoing regulatory requirements after
    receipt of approval to commercialize a product, we 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;
    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
    violate healthcare statutes such as fraud and abuse laws, we
    could be subject to significant penalties and
    expenses.
     32




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and/or
    and/or
    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.
   33




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
    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;
    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 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 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.     34




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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 product 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 product
    candidates and the commercialization of any products that we
    successfully develop could be harmed.
  ® ®
  co-promote ® ® ® ® ® ® ® ®
 35




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Novartis
    has the option to license from us product candidates we
    discover, or in some cases, acquire. If Novartis does not
    exercise its option with respect to a product candidate, our
    development, manufacture and/or commercialization of such
    product 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.
     36




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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 product
    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.   37




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
    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
    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 product candidates
    licensed to Novartis and the development and commercialization
    of our other product candidates could be delayed, curtailed or
    terminated.
  co-promote ® ®
    Novartis
    has the right under certain circumstances to market and sell
    products that compete with the product candidates and products
    that we license to it, and any competition by Novartis could
    have a material adverse effect on our business.
    
    this agreement not to compete extends only until May 2008;
    as to any country, the agreement not to compete would terminate
    if Novartis terminates the development and commercialization
    agreement with respect to that country; and
    if Novartis wishes to market, sell, promote or license a
    competitive product, it is required to inform us of the
    competitive product opportunity and, at our election, enter into
    good faith negotiations with us concerning such opportunity. If
    we either do not elect to enter into negotiations with respect
    to such opportunity or are 38




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unable to reach agreement within a specified period, Novartis
    would be free to proceed with its plans with respect to such
    competing product.    Factors
    Related to Our Dependence on Third Parties
  If we
    seek to enter into collaboration agreements for any product
    candidates other than those licensed to Novartis and we are not
    successful in establishing such collaborations, we may not be
    able to continue development of those product
    candidates.
    and/or
  
    we may be required to expend our own funds to advance the
    product candidate to commercialization;
    revenue from product sales could be delayed; or
    we may elect not to develop or commercialize the product
    candidate.  If any
    collaborative partner terminates or fails to perform its
    obligations under agreements with us, the development and
    commercialization of our product candidates could be delayed or
    terminated.
    Our
    collaborations with outside scientists may be subject to
    restriction and change.
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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.
      and/or
  Factors
    Related to Patents and Licenses
  If we
    are unable to adequately protect our patents and licenses
    related to our product 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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®
    ® ®
  ® ®
    42




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® ®
        
    ownership of patents and patent applications;
    the patentability of our inventions relating to our product
    candidates; and/or 43




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
    the enforceability, validity or scope of protection offered by
    our patents relating to our product candidates.          
    incur substantial monetary damages;
    encounter significant delays in bringing our product candidates
    to market; and/or
    be precluded from participating in the manufacture, use or sale
    of our product 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.
    If any
    of our agreements that grant us the exclusive right to make, use
    and sell our product candidates are terminated, we and/or
    Novartis may be unable to develop or commercialize our product
    candidates.
  ® ® ® ®
 44




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co-owned
    If our
    cooperative research agreement with the University of Cagliari
    is terminated, 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.
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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
    and, to the extent applicable, other licensing and collaborative
    agreements;
    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 product candidates;
    the results of ongoing and planned clinical trials of our
    product candidates;
    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 product 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
    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;
    the results of discovery, preclinical studies and clinical
    trials by us or our competitors;
    the acquisition of technologies, product candidates or products
    by us or our competitors;
    the development of new technologies, product candidates or
    products by us or our competitors;
    regulatory actions with respect to our product 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; 46




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##### Table of Contents




    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.
    Item 1B.
    Unresolved
    Staff Comments.    Item 2.
    Properties.    Approximate Square




LeaseProperty Location

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.  ® ®
 47




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##### Table of Contents



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


Low2006First quarter

$
23.87


$
13.17Second quarter

$
13.76


$
7.50Third quarter

$
11.21


$
8.56Fourth quarter

$
10.49


$
8.052007First quarter

$
10.83


$
7.18Second quarter

$
8.24


$
5.76Third quarter

$
6.07


$
2.29Fourth quarter

$
3.30


$
2.10   Stockholders
    Dividends
    Repurchase
    of Securities
   48




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##### Table of Contents



Item 6.
    Selected
    Consolidated Financial Data  Form 10-K. Form 10-K,
  Years Ended December 31,2007


2006


2005


2004


2003(In thousands, except per share data)Consolidated Statement of Operations Data:Revenues

$
68,028


$
67,377


$
64,718


$
95,389


$
29,570Operating expensesCost of sales


2,001



62











Research and development


85,839



96,080



86,590



79,979



51,477Selling, general and administrative


63,348



56,954



33,657



23,603



20,193Restructuring and impairment charges


8,744















Total operating expenses


159,932



153,096



120,247



103,582



71,670Loss from operations


(91,904
)


(85,719
)


(55,529
)


(8,193
)


(42,100
)Investment and other income, net


6,387



9,487



4,038



1,383



404Gain on sale of equity securities


3,500















Income tax benefit (expense)


(498
)


1,145



714



566



(184
)Net loss


(82,515
)


(75,087
)


(50,777
)


(6,244
)


(41,880
)Accretion of redeemable convertible preferred stock


















(29,074
)Net loss attributable to common stockholders

$
(82,515
)

$
(75,087
)

$
(50,777
)

$
(6,244
)

$
(70,954
)Basic and diluted net loss per common share

$
(1.47
)

$
(1.34
)

$
(1.03
)

$
(0.15
)

$
(2.70
)Shares used in computing basic and diluted net loss per common
    share


56,169



56,005



49,395



41,369



26,232   As of December 31,2007


2006


2005


2004


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

$
48,260


$
55,892


$
83,733


$
42,083


$
43,485Working capital


72,985



110,159



167,069



70,123



30,399Total assets


160,540



228,465



277,657



187,118



67,090Deferred revenue, current


















107Deferred revenue, net of current portion


4,272



4,272



4,272



4,272



4,272Deferred revenue, related party, current


8,372



13,490



9,695



9,695



10,756Deferred revenue, related party, net of current portion


41,861



40,471



29,089



38,779



54,239Long-term obligations


13,172



2,251



2,792



3,691



4,849Accumulated deficit


(438,756
)


(355,941
)


(280,854
)


(230,077
)


(223,833
)Total stockholders equity (deficit)


68,838



142,025



206,887



109,058



(27,731
)  49




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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
    ® ® ® ® ®
  ® ® ® ®
  ® ®
 50




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##### Table of Contents



® ®
  Indication

Product/Product Candidates/Programs

DescriptionHBV

Tyzeka®/Sebivo®*
    (telbivudine)
    (L- nucleoside)

Effective October 1, 2007, we transferred to Novartis all of our
    development, commercialization and manufacturing rights and
    obligations related to telbivudine
    (Tyzeka®/Sebivo®)
    on a worldwide basis in exchange for royalty payments equal to a
    percentage of net sales of
    Tyzeka®/Sebivo®.
    Beginning in the fourth quarter of 2007, Novartis is solely
    responsible for clinical trial costs and related expenditures
    associated with telbivudine. We have transitioned to Novartis
    all ongoing clinical trials and commercial activities related to
    telbivudine.valtorcitabine
    (L-nucleoside)

During the third quarter of 2007, we discontinued development of
    valtorcitabine.HCV

valopicitabine (NM283) 
    (Nucleoside analog)

In July 2007, this program was placed on clinical hold by the
    FDA and development of the program was discontinued.discovery program

Preclinical evaluation of compounds from the HCV discovery
    program is in progress. 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. Nucleoside/nucleotide polymerase
    inhibitors
    (IDX184 and IDX102)

The most advanced of these efforts is our research in
    next-generation nucleoside/nucleotide polymerase inhibitors.
    IDX184 and IDX102 are in late stage preclinical development. We
    expect to submit an IND in the United States and a CTA in Europe
    for at least one of these product candidates in 2008. Protease inhibitors

We are evaluating multiple scaffolds in our protease inhibitor
    discovery program. Clinical candidates from this program have
    been selected and IND-enabling pharmacology and toxicology
    studies are ongoing. Non-nucleoside polymerase inhibitors

We have an ongoing discovery effort in non-nucleoside polymerase
    inhibitors. 51




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##### Table of Contents



Indication

Product/Product Candidates/Programs

DescriptionHIV

IDX899 (Non-nucleoside reverse
    transcriptase
    inhibitor or NNRTI)

In addition to our HCV discovery and development program, we are
    also engaged in efforts to develop therapeutics for the
    treatment of HIV-1 from the class of compounds known as
    non-nucleoside reverse transcriptase inhibitors, or NNRTIs. This
    class of drugs is being evaluated for once-a-day oral
    administration. We filed an IND for IDX899 in 2007 and completed
    a phase I dose escalation study in healthy volunteers.  The
    phase I study was designed to assess the safety and
    pharmacokinetics of IDX899 in healthy volunteers. In this study,
    IDX899 appeared to be well tolerated at single doses up to
    1200 mg and multiple doses up to 800 mg daily over a
    seven day period. No serious or clinically significant adverse
    events were reported for the 65 IDX899-treated volunteers in
    this study. One healthy volunteer, after the 400 mg single
    dose administration of this study, experienced a single
    unconfirmed QTc elevation.  We believe this is not a significant
    clinical finding as it is within the expected variability of
    multiple QTc measurements in a healthy volunteer study. Two
    volunteers discontinued from the study due to adverse events.   ® ® ® ®
  ® ®
   52




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##### Table of Contents



® ® ® ® ® ®
  ® ® ® ®
    ® ®
  ® ® ® ® ® ® ® ®
   53




---



##### Table of Contents



® ®
    ® ®
  Period fromMay 1,1998(Inception)Disease

Product/Product

Through


Years Ended December 31,Indication

Candidate

December 31, 2003


2004


2005


2006


2007


Total(Dollars in thousands)HBV


Tyzeka®/Sebivo®

$
41,519


$
43,483


$
46,447


$
36,310


$
24,147


$
191,906HBV


Valtorcitabine


8,338



8,673



3,770



3,726



1,515



26,022HCV


Valopicitabine


8,947



7,096



12,140



11,489



6,196



45,868$
58,804


$
59,252


$
62,357


$
51,525


$
31,858


$
263,796     Estimated AdditionalAmount ofDirect/Third-PartyResearch andDevelopment ExpensesExpected tobe IncurredPrior toCurrent Stage of

Commercial LaunchProduct Candidate

Development

of a DrugIDX102 and IDX184

preclinical

$
200 to $500 millionProtease Inhibitor Program

preclinical

$
200 to $500 millionIDX899

clinical

$
200 to $300 million   project-by-project project-by-project
 54




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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



12,049Milestone revenue


10,000



Royalty revenue


617



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 product candidates, net of certain qualifying costs incurred
    by Novartis;
    license and other fees received from Novartis for the license of
    HBV and HCV product candidates, net of reductions for Novartis
    stock subscription rights, which is being recognized over the
    development period of the licensed product 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 outside of 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 55




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##### Table of Contents



® ® ® ® ® ®
  ®
  Cost
    of Sales
    Research
    and Development Expenses
  ® ® ®
    Selling,
    General and Administrative Expenses
  ® ®
    Restructuring
    and Impairment Charges
  ® ®
 56




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##### Table of Contents



Investment
    and Other Income, Net
    Gain
    on Sale of Equity Securities
    Income
    Taxes
  Accounting for
    Uncertain Tax Positions.
  Comparison
    of Years Ended December 31, 2006 and 2005
  Revenues
    2006


2005(In thousands)Collaboration revenue  related partyReimbursement of research and development costs

$
54,858


$
54,718License fee revenue


12,049



9,700Substantive milestone revenue






Profit-sharing to related party


(183
)


66,724



64,418Product sales, net


424



Government grants


229



300Total revenues

$
67,377


$
64,718     Research
    and Development Expenses
   57




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##### Table of Contents



Share-Based Payment,
  Selling,
    General and Administrative Expenses
  ® ®
  Investment
    and Other Income, Net
    Income
    Taxes
    Liquidity
    and Capital Resources
  ® ® ® ® ®
  available-for-sale.
   58




---



##### Table of Contents



mortgage-backed. mid-February short-term
  ® ®
        Current LiabilityYear Ended December 31, 2007


at December 31,Charge


Payments/Settlements


2007(In thousands)Employee severance, benefits and related costs

$
6,492


$
(4,654
)

$
1,838Contract termination and other costs


139



(139
)


Total

$
6,631


$
(4,793
)

$
1,838    59




---



##### Table of Contents



Payments Due by PeriodLess


One


ThreeThan


to


to


AfterOne


Three


Five


FiveContractual Obligations

Total


Year


Years


Years


YearsOperating leases

$
17,355


$
3,228


$
5,654


$
4,141


$
4,332Consulting and other agreements


5,810



2,345



3,428



37



Total contractual obligations

$
23,165


$
5,573


$
9,082


$
4,178


$
4,332              60




---



##### Table of Contents



® ®
         61




---



##### Table of Contents



® ®
  Off-Balance
    Sheet Transactions
    Critical
    Accounting Policies and Estimates
      Collaborative
    Research and Development Revenue
  Revenue
    Recognition in Financial Statements,
    ® ®
 62




---



##### Table of Contents



® ®
    24-month
     63




---



##### Table of Contents




    the milestone is non-refundable;
    achievement of the milestone was not reasonably assured at the
    inception of the arrangement;
    substantive effort is involved to achieve the milestone; and
    the amount of the milestone appears reasonable in relation to
    the effort expended, the other milestones in the arrangement and
    the related risk associated with the achievement of the
    milestone.  ® ®
 64




---



##### Table of Contents



No. 00-21, Accounting for Revenue Arrangements with Multiple
    Deliverables, No. 00-21. No. 00-21 and/or No. 00-21
  Valuation
    and Impairment of Investments and/or Marketable
    Securities
  and/or
    
    the duration of the period that, and the extent to which, the
    fair value is less than cost basis;
    the financial health of and business outlook for the issuer,
    including industry and sector performance and operational and
    financing cash flow factors; and
    overall market conditions and trends.    Accrued
    Expenses
   65




---



##### Table of Contents



Stock-Based
    Compensation
  Share-Based Payment Accounting for Stock-Based
    Compensation, Accounting for
    Stock Issued to Employees,
    Transition Election Related to
    Accounting for Tax Effects of Share-based Payment Awards,
       66




---



##### Table of Contents



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
      Recent
    Accounting Pronouncements
  Fair
    Value Measurements,
  FASB Staff Position
    No. FAS 157-2,
    Effective Date of FASB Statement No. 157 FAS 157-2. FAS 157-2
  The Fair
    Value Option for Financial Assets and Financial
    Liabilities, Accounting for Certain Investments in
    Debt and Equity Securities,
  No. 07-03, Accounting for Nonrefundable Advance Payment for Goods
    and Services Received for Use in Future Research and Development
    Activities, EITF 07-03 EITF 07-03 EITF 07-03
 67




---



##### Table of Contents



No. 07-01, Accounting for Collaborative Arrangements Related to
    the Development and Commercialization of Intellectual
    Property EITF 07-01, 07-01 EITF 07-01
  Item 7A.
    Quantitative
    and Qualitative Disclosure about Market Risk.          Item 8.
    Financial
    Statements and Supplementary Data.  Form 10-K.
  Item 9.
    Changes
    in and Disagreements With Accountants on Accounting and
    Financial Disclosure.   68




---



##### 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.
     69




---



##### Table of Contents



Changes
    in Internal Control Over Financial Reporting
  Rules 13a-15(f) 15d-15(f)
  Item 9B.
    Other
    Information.   70




---



##### 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   71




---



##### Table of Contents



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


73Consolidated Balance Sheets at December 31,
    2007 and 2006


74Consolidated Statements of Operations for the
    Years Ended December 31, 2007, 2006 and 2005


75Consolidated Statements of Stockholders
    Equity and Comprehensive Loss for the Years Ended
    December 31, 2007, 2006 and 2005


76Consolidated Statements of Cash Flows for the
    Years Ended December 31, 2007, 2006 and 2005


77Notes to the Consolidated Financial Statements


78   (a)(2) Financial Statement Schedules.
  (a)(3) Exhibits. Form 10-K
 72




---



##### Table of Contents



Report of
    Independent Registered Public Accounting Firm     Internal Control  Integrated
    Framework
        PricewaterhouseCoopers
    LLP
    73




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    BALANCE SHEETS
  December 31,2007


2006(In thousands,except share data)ASSETSCurrent assets:Cash and cash equivalents

$
48,260


$
55,892Restricted cash


411



411Marketable securities


39,862



71,251Accounts receivable, net






509Receivables from related party


11,196



12,035Income taxes receivable


224



201Inventory






400Prepaid expenses and other current assets


3,766



6,906Total current assets


103,719



147,605Intangible asset, net


13,548



Property and equipment, net


15,460



17,448Restricted cash, non-current


750



750Marketable securities, non-current


23,882



59,208Income taxes receivable, non-current


2,296



2,060Investment






500Other assets


885



894Total assets

$
160,540


$
228,465LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable

$
5,372


$
6,811Accrued expenses


16,437



15,679Payables to related party






939Deferred rent


338



338Deferred revenue, related party


8,372



13,490Income taxes payable


215



189Total current liabilities


30,734



37,446Long-term obligations


13,172



2,251Deferred rent, net of current portion


1,663



2,000Deferred revenue


4,272



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


41,861



40,471Total liabilities


91,702



86,440Commitments and contingencies (Note 13 and 19)Stockholders equity:Common stock, $0.001 par value; 125,000,000 and
    75,000,000 shares authorized at December 31, 2007 and
    2006; 56,189,467 and 56,091,632 shares issued and
    outstanding at December 31, 2007 and 2006, respectively


56



56Additional paid-in capital


506,800



497,778Deferred compensation






(106
)Accumulated other comprehensive income


738



238Accumulated deficit


(438,756
)


(355,941
)Total stockholders equity


68,838



142,025Total liabilities and stockholders equity

$
160,540


$
228,465    74




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF OPERATIONS
  Years Ended December 31,2007


2006


2005(In thousands, except per share data)Revenues:License fees and collaborative research and development -
    related party

$
64,751


$
66,724


$
64,418Product sales, net


3,187



424



Government research grants


90



229



300Total revenues


68,028



67,377



64,718Operating expenses:Cost of sales


2,001



62



Research and development


85,839



96,080



86,590Selling, general and administrative


63,348



56,954



33,657Restructuring and impairment charges


8,744







Total operating expenses


159,932



153,096



120,247Loss from operations


(91,904
)


(85,719
)


(55,529
)Investment and other income, net


6,387



9,487



4,038Gain on sale of equity securities


3,500







Loss before income taxes


(82,017
)


(76,232
)


(51,491
)Income tax (expense) benefit


(498
)


1,145



714Net loss

$
(82,515
)

$
(75,087
)

$
(50,777
)Basic and diluted net loss per common share

$
(1.47
)

$
(1.34
)

$
(1.03
)Shares used in computing basic and diluted net loss per common
    share


56,169



56,005



49,395    75




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##### Table of Contents





IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF STOCKHOLDERS EQUITY AND COMPREHENSIVE
    LOSS
 For
    the Years Ended December 31, 2007, 2006, 2005
  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, 2004


47,857,887


$
48


$
340,938


$
(1,987
)

$
136


$
(230,077
)

$
109,058Issuance of common stock in follow-on public offering, net of
    offering expenses and underwriting discounts of $4,567


3,338,889



3



64,245















64,248Issuance of common stock in follow-on public offering, with
    related party


3,939,131



4



81,181















81,185Compensation related to modification of employee stock options










98















98Issuance of common stock upon exercise of stock options


590,618



1



2,017















2,018Issuance of common stock upon vesting of stock options


86,750







255















255Forfeiture of common stock under stock option plans










(385
)


385











Amortization of deferred compensation














1,282











1,282Antidilution shares contingently issuable to related party










(9
)














(9
)Net loss






















(50,777
)


(50,777
)

$
(50,777
)Net change in unrealized holding gains on marketable securities,
    net of tax


















119







119



119Cumulative translation adjustment


















(590
)






(590
)


(590
)Comprehensive loss





























$
(51,248
)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















892Issuance of common stock upon vesting of stock options


14,442







44















44Issuance of common stock with related party


3,303







54















54Stock-based compensation for non-employees










30















30Amortization of deferred compensation










8,393



214











8,607Antidilution shares contingently issuable to related party










25















25Net 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















205Amortization of deferred compensation










8,625



106











8,731Antidilution shares contingently issuable to related party










192















192Cumulative 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
)

$
68,838
    76




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##### Table of Contents





IDENIX
    PHARMACEUTICALS, INC.
  CONSOLIDATED
    STATEMENTS OF CASH FLOWS
  Years Ended December 31,2007


2006


2005(In thousands)Cash flows from operating activities:Net loss

$
(82,515
)

$
(75,087
)

$
(50,777
)Adjustments to reconcile net loss to net cash used in operating
    activities:Depreciation and amortization


8,955



3,463



2,066Stock-based compensation expense


8,731



8,637



1,388Impairment charges


2,113







Gain on sale of equity securities


(3,500
)






Accrued interest on marketable securities


338



(1,319
)


(991
)Other


128



12



3Changes in operating assets and liabilities:Accounts receivables


509



(509
)


Receivables from related party


839



1,688



2,520Inventory


400



(400
)


Prepaid expenses and other current assets


3,311



(753
)


(2,992
)Income taxes receivable


(82
)


(1,347
)


(576
)Other assets


10



1,076



(26
)Accounts payable


(1,468
)


1,146



1,154Accrued expenses


(3,596
)


(982
)


1,718Payables to related party


(773
)


939



Deferred rent


(338
)


(28
)


860Deferred revenue, related party


(3,618
)


15,189



(9,697
)Income taxes payable


(10
)


(17
)


(104
)Long-term obligations


(113
)


(541
)


(865
)Net cash used in operating activities


(70,679
)


(48,833
)


(56,319
)Cash flows from investing activities:Purchase of property and equipment


(7,299
)


(9,561
)


(6,586
)Purchases of marketable securities


(92,702
)


(243,011
)


(155,963
)Sales and maturities of marketable securities


159,017



272,496



113,824Proceeds from sale of equity securities of Pharmasset, Inc


4,000







Restricted deposits










(411
)Net cash provided by (used in) investing activities


63,016



19,924



(49,136
)Cash flows from financing activities:Net proceeds from sale of common stock in public offerings and
    private placements, net of offering costs










145,433Proceeds from exercise of common stock options


205



902



2,018Proceeds from issuance of common stock to related party






54



Net cash provided by financing activities


205



956



147,451Effect of changes in exchange rates on cash and cash equivalents


(174
)


112



(346
)Net (decrease) increase in cash and cash equivalents


(7,632
)


(27,841
)


41,650Cash and cash equivalents at beginning of year


55,892



83,733



42,083Cash and cash equivalents at end of year

$
48,260


$
55,892


$
83,733Supplemental disclosure of cash flow information:Taxes paid

$
196


$
144


$
53Supplemental disclosure of noncash investing and financing
    activities:Value of shares of common stock contingently issuable or issued
    to related party


192



25



(9
)Accrued proposed settlement amount


15,000







    77




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL STATEMENTS
  1.
    Organization
    and Business      ® ® ® ®
    ® ® ® ®
  ® ®
   78




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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
    ®
  Marketable
    Securities
   79




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Fair
    Value of Financial Instruments
    Inventory
  first-in, ® ®
  Investment
  Accounting
    for Certain Investments in Debt and Equity Securities
 80




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Intangible
    Asset
      Property
    and Equipment
    Impairment
    of Long-Lived Assets
  Accounting for the Impairment of Disposal of Long-Lived
    Assets construction-in-progress
  Revenue
    Recognition
    Collaborative Research and Development
    Revenue
 81




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      No. 00-21, Accounting for Revenue Arrangements with Multiple
    Deliverables No. 00-21). No. 00-21 and/or No. 00-21
      Product Sales ® ®
 82




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  ®
  ® ® ®
  Government Research Grant Revenue
  Research
    and Development Expenses
    Patents
    Share-Based
    Compensation
  Share-Based Payment Accounting for
    Stock-Based Compensation, Accounting for Stock Issued to Employees.
    Transition Election Related to
    Accounting for Tax Effects of Share-based Payment Awards,
 83




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    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
    Income (Loss)
   84




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  Net
    Income (Loss) per Common Share
  Earnings Per Share
  Segment
    Reporting
  Disclosures About Segments of
    an Enterprise and Related Information
  3.
    Novartis
    Relationship  Overview
    ® ® ® ®
  ® ® ® ® ® ®
 85




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      ® ® ® ® ® ®
      ® ® ® ®
   86




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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
   87




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Manufacturing
    and Packaging Agreements
  ® ®
  ® ®
  Product
    Sales Arrangements
    ® ® ®
 88




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  ®
  ® ® ®
  ® ®
  4.
    Public
    Offerings of Common Stock  Public
    Offering of Common Stock
    
    the Company issued and sold 7,278,020 shares of its common
    stock; and
    certain stockholders sold 942,507 shares of the
    Companys common stock.    5.
    Net Loss
    Per Common Share    Years Ended December 31,2007

2006

2005(In thousands, except per share data)Basic and diluted net loss per common share:Net loss

$
(82,515
)

$
(75,087
)

$
(50,777
)Basic and diluted weighted average number of common shares
    outstanding


56,169



56,005



49,395Basic and diluted net loss per common share

$
(1.47
)

$
(1.34
)

$
(1.03
)     Years Ended December 31,2007

2006

2005(In thousands)Options


5,712



4,387



3,584Contingently issuable shares to related party


790



77



26Restricted stock










11   6.
    Marketable
    Securities  Accounting for Certain
    Investments in Debt and Equity Securities.
 89




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    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, 2006Gross Unrealized


Gross UnrealizedAmortized Cost


Gains


Losses


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

$
13,940


$



$



$
13,940Commercial paper


5,988











5,988Corporate debt securities


111,486



17



(53
)


111,450U.S. Treasury securities and obligations of U.S. government
    agencies


9,176



2



(11
)


9,167Taxable auction rate securities


8,511



14



(2
)


8,523Accrued interest


1,371











1,371$
150,472


$
33


$
(66
)

$
150,439   December 31,


December 31,2007


2006(In thousands)Contractual maturity:Maturing in one year or less

$
69,883


$
91,231Maturing after one year through two years


4,490



16,310Maturing after two years through ten years


7,274



24,922Maturing after ten years


12,118



17,976$
93,765


$
150,439    90




---



##### Table of Contents



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


December 31,2007


2006(In thousands)Classification in balance sheets:Cash equivalents

$
30,021


$
19,980Marketable securities


39,862



71,251Marketable securities, non-current


23,882



59,208$
93,765


$
150,439     7.
    Receivables
    from Related Party    December 31,2007

2006(In thousands)Unbilled receivables from related party

$
11,196


$
12,035    91




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  8.
    Property
    and Equipment, Net    EstimatedUsefulLife


December 31,(Years)


2007


2006(In thousands)Office equipment


5


$
67


$
71Scientific equipment


7



6,958



5,738Computer equipment and software


2



3,787



4,005Enterprise software


5



2,599



2,307Office furniture


7



1,575



1,645Trade show booths


2







382Leasehold improvements


*



11,043



7,540Construction-in-progress






60



3,94426,089



25,632Less  accumulated depreciation






(10,629
)


(8,184
)$
15,460


$
17,448     *
    
    Shorter of asset life or lease term.  Construction-in-progress
  construction-in-progress
  9.
    Accrued
    Expenses    December 31,2007


2006(In thousands)Research and development contract costs

$
2,050


$
5,502Payroll and benefits


4,231



5,676License fees


1,000



1,000Professional fees


1,309



753Restructuring


1,838



Accrued proposed settlement amount


4,000



Other


2,009



2,748$
16,437


$
15,679  92




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##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      10.
    Restructuring
    and Impairment Charges  ® ® ® ®
  Current LiabilityYear Ended December 31, 2007


at December 31,Charge


Payments/Settlements


2007(In thousands)Employee severance, benefits and related costs

$
6,492


$
(4,654
)

$
1,838Contract termination and other costs


139



(139
)


Total

$
6,631


$
(4,793
)

$
1,838     11.
    Common
    Stock          12.
    Equity
    Incentive Plans and Share-Based Compensation   93




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
         94




---



##### Table of Contents



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


Number


WeightedOptions Available


of Options


Averagefor Future Grant


Outstanding


Exercise PriceOutstanding, December 31, 2004


749,258



3,161,790


$
7.50Granted






1,167,750


$
20.27Exercised






(590,618
)

$
3.42Cancelled






(154,600
)

$
10.67Outstanding, December 31, 2005


338,608



3,584,322


$
12.20Granted






1,373,187


$
14.50Exercised






(263,804
)

$
3.42Cancelled






(306,944
)

$
17.84Outstanding, December 31, 2006


869,869



4,386,761


$
13.05Granted






2,568,956


$
5.19Exercised






(97,835
)

$
2.09Cancelled






(1,145,593
)

$
12.36Outstanding, December 31, 2007


2,446,506



5,712,289


$
9.83Exercisable, December 31, 2006






2,483,361


$
11.16Exercisable, December 31, 2007






3,298,337


$
11.78           Years Ended December 31,2007


2006


2005(In thousands)Research and development

$
3,005


$
2,892


$
722Selling, general and administrative


4,758



5,745



666Restructuring and impairment


968







Total stock-based compensation expense

$
8,731


$
8,637


$
1,388  95




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      2007

2006

2005Expected dividend yield










Risk-free interest rate


4.35
%


4.78
%


3.94
%Expected option term (in years)


5.1



5.0



5.0Expected volatility


59.5
%


63.0
%


83.0
%         Year EndedDecember 31, 2005(In thousands,except per share data)Net loss  as reported

$
(50,777
)Add stock-based employee compensation expense included in
    reported net loss


1,388Deduct stock-based compensation expense determined under fair
    value based method


(7,216
)Net loss  pro forma

$
(56,605
)Net loss per common share (basic and diluted)As reported

$
(1.03
)Pro forma


(1.15
)  96




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  13.
    Commitments
    and Contingencies  Lease
    Arrangements
    OperatingYear Ending December 31,

Leases(In thousands)2008

$
3,2282009


3,3322010


2,3222011


2,0922012


2,0492013 and thereafter


4,332Total

$
17,355       48-month
  Legal
    Contingencies
  Hepatitis
    C Product Candidates
   97




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      Hepatitis
    B Product
     98




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
      ® ®
  Indemnification
   99




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  14.
    Income
    Taxes    2007


2006


2005(In thousands)Loss before income taxesU.S

$
(82,210
)

$
(61,877
)

$
(26,400
)Foreign


193



(14,355
)


(25,091
)$
(82,017
)

$
(76,232
)

$
(51,491
)Income tax expense (benefit)CurrentFederal  U.S

$
(257
)

$
(48
)

$
State  U.S


176



135



51Foreign


579



(1,232
)


(765
)498



(1,145
)


(714
)DeferredFederal  U.S

$



$



$
State  U.S










Foreign


















Total income tax expense (benefit)

$
498


$
(1,145
)

$
(714
)      100




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    2007


2006(In thousands)Depreciation

$
132


$
(337
)Development contracts


1,909



2,740Nonqualified stock options


3,350



1,788Deferred licensing income


16,320



10,644Accrued expenses and other


3,586



1,244Capitalized research costs


28,842



32,986Research and development credits


5,555



5,555Foreign tax credit carryforward


1,326



877Net operating carryforwards


64,204



41,045Valuation allowance


(125,224
)


(96,542
)Deferred tax asset

$



$
     2007

2006

2005Federal statutory rate benefit


(34
)%


(34
)%


(34
)%Foreign tax expense (benefit)






(1
)


(2
)State tax benefit, net of federal benefit


(4
)


(10
)


(6
)Permanent items


1



(35
)


(13
)Foreign rate differentials






7



17Valuation allowance


38



72



37Effective income tax rate


1
%


(1
)%


(1
)%        101




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    Accounting for
    Income Taxes
          Balance at January 1, 2007

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


459Additions for tax positions of prior periods


1,324Reductions for tax positions for closing of statute of
    limitations


(6,877
)Settlements


Balance at December 31, 2007

$
2,840      102




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
          15.
    Employee
    Benefit Plans        16.
    Related
    Party Transactions    ®
   103




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
  17.
    Segment
    Reporting    2007


2006(In thousands)United States

$
11,530


$
14,198Europe


3,930



3,250$
15,460


$
17,448   18.
    Licensing
    Agreements  UAB
    Research Foundation
      19.
    Collaborative
    Agreements and Contracts  Le
    Centre National de la Recherche Scientifique and
    LUniversite Montpellier II
    Universita
    di Cagliari
   104




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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
   105




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##### Table of Contents



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

Second

Third

Fourth

TotalQuarter

Quarter

Quarter

Quarter

Year(In thousands, except per share amounts)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
)2006Total revenues

$
13,111


$
19,313


$
19,645


$
15,308


$
67,377Total operating expenses


32,708



37,025



42,007



41,356



153,096Net loss


(17,182
)


(14,609
)


(19,715
)


(23,581
)


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


(0.31
)


(0.26
)


(0.35
)


(0.42
)


(1.34
)   21.
    Recent
    Accounting Pronouncements  Fair
    Value Measurements,
 106




---



##### Table of Contents



IDENIX
    PHARMACEUTICALS, INC.
  NOTES TO
    THE CONSOLIDATED FINANCIAL
    STATEMENTS  (Continued)
    FASB Staff Position
    No. FAS 157-2,
    Effective Date of FASB Statement No. 157 FAS 157-2. FAS 157-2
  The Fair
    Value Option for Financial Assets and Financial
    Liabilities Accounting for Certain
    Investments in Debt and Equity Securities
  No. 07-03, Accounting for Nonrefundable Advance Payment for Goods
    and Services Received for Use in Future Research and Development
    Activities (EITF 07-03) EITF 07-03 EITF 07-03
  No. 07-01, Accounting for Collaborative Arrangements Related to
    the Development and Commercialization of Intellectual
    Property EITF 07-01, 07-01 EITF 07-01
 107




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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 14, 2008/s/  Ronald
    C. Renaud, Jr.Ronald
    C. Renaud, Jr.

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

March 14, 2008/s/  Charles
    CrambCharles
    Cramb

Director

March 14, 2008/s/  Wayne
    HockmeyerWayne
    Hockmeyer

Director

March 14, 2008/s/  Thomas
    HodgsonThomas
    Hodgson

Director

March 14, 2008/s/  Norman
    PaysonNorman
    Payson

Director

March 14, 2008/s/  Robert
    PelzerRobert
    Pelzer

Director

March 14, 2008/s/  Denise
    Pollard-KnightDenise
    Pollard-Knight

Director

March 14, 2008/s/  Emmanuel
    PuginierEmmanuel
    Puginier

Director

March 14, 2008/s/  Pamela
    Thomas-GrahamPamela
    Thomas-Graham

Director

March 14, 2008  108




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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

*3.5

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 109




---



##### 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+

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



333-11115710.12+

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



333-11115710.13+

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



333-11115710.14+

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



333-11115710.15+

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



000-4983910.16+

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



000-4983910.17+

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



000-4983910.18+

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



000-49839 110




---



##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.19

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



000-4983910.20

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



000-4983910.21+

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



333-1111510.22

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



000-4983910.23+

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



000-4983910.24+

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



000-49839University of Cagliari10.25+

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



333-11115710.26+

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

S-1


10
.17


12/15/2003



333-11115710.27+

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



333-11115710.28+

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



333-11115710.29

Collaborative Activities Agreement, dated March 22, 2004,
    by and between the Registrant and the University of Cagliari, as
    amended June 30, 2004 (English translation)

S-1 Amendment 3


10
.18.2


7/6/2004



333-11115710.30+

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

10-Q for 
    9/30/2005


10
.1


11/08/2005



000-49839 111




---



##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

NumberMiscellaneous10.31+

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



333-11115710.32

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

S-1


10
.20


12/15/2003



333-11115710.33+

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

S-1


10
.21


12/15/2003



333-11115710.34+

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



333-11115710.35

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



333-11115710.36+

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



333-11115710.37

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

S-1


10
.13


12/15/2003



333-11115710.38

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



333-111157Material contracts  management contracts and
    compensatory plans10.39#

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



000-4983910.41#

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

8-K


10
.3


6/13/2005



000-4983910.41#

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



000-49839 112




---



##### Table of Contents



Incorporated by Reference toSECExhibit





Exhibit

Filing

FileNumber

Description

Form

No.

Date

Number10.42#

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



000-4983910.43#

2005 Stock Incentive Plan

8-K


10
.4


6/13/2005



000-4983910.44#

2004 Stock Incentive Plan

S-1 Amendment 2


10
.32


5/28/2004



333-11115710.45#

Amended and Restated 1998 Equity Incentive Plan

S-1 Amendment 2


10
.1


5/28/2004



333-11115710.46#

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

S-1


10
.5


12/15/2003



333-11115710.47#

Employment Agreement, dated July 28, 2003, by and between
    the Registrant and Guy Macdonald

S-1


10
.10


12/15/2003



333-11115710.48#

Letter Agreement, dated September 1, 2006, by and between
    the Registrant and Guy Macdonald

8-K


10
.3


9/8/2006



000-4983910.49#

Letter Agreement, dated October 19, 2007, by and between
    the Registrant and Guy Macdonald

8-K


10
.1


10/22/2007



000-4983910.50#

Summary of Relocation Adjustment, effective as of
    December 8, 2005, between the Registrant and Guy Macdonald

10-K for
    12/31/2005


10
.48


3/16/2006



000-4983910.51#

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

8-K


10
.1


9/8/2006



000-4983910.52#

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

8-K


10
.1


5/8/2007



000-4983910.53#

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

8-K


10
.1


6/19/2007



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

* 113




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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 114