##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549
 
 FORM 10-K/A Amendment No. 1 to Form 10-K
For Annual and Transition Reports Pursuant to
Sections 13 or 15(d) of the Securities Exchange Act of 1934
 (Mark One) þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2004 OR o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period fromto Commission file number 000-49839 
 Idenix Pharmaceuticals, Inc.  Delaware
(State or Other Jurisdiction of
Incorporation or Organization)
    
    45-0478605
(I.R.S. Employer
Identification No.)
 60 Hampshire Street,
Cambridge, Massachusetts
(Address of Principal Executive Offices)
    
    02139
(Zip Code)
 Registrants telephone number, including area code:(617) 995-9800 Securities registered pursuant to Section 12(b) of the Act: NONE Securities registered pursuant to Section 12(g) of the Act: Common Stock, $.001 par value
(Title of class) 
 Indicate by check mark whether the registrant: (1) has filed all reports required to be filed
by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or
for such shorter period that the registrant was required to file such reports), and (2) has been
subject to such filing requirements for the past 90 days. Yes þ   No o Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation
S-K is not contained herein, and will not be contained, to the best of registrants knowledge, in
definitive proxy or information statements incorporated by reference in Part III of this Form 10-K
or any amendment to the Form 10-K. þ Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule
12b-2 of the Exchange Act) Yes o No þ The aggregate market value of the voting common stock held by nonaffiliates of the registrant
based, on the last reported sale price of the common stock on the NASDAQ Stock Market on April 15,
2005, was approximately $233,369,538. For this purpose, shares of
voting stock held by each executive officer,
director and stockholder known to the registrant holding 5% or more of the registrants voting
stock have been excluded in that such persons may be deemed to be affiliates. Number of shares outstanding of the registrants class of common stock as of April 15, 2005:
48,149,768 shares.




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EXPLANATORY NOTE This
Amendment No. 1 (this Amendment) on Form 10-K/A of Idenix Pharmaceuticals, Inc.
(the Registrant, the Company, Idenix, we, or us) to the Registrants Annual Report on
Form 10-K is being filed for the purposes of amending Items 10, 11, 12, 13 and 14 therein to
include previously omitted information required to be set forth in
Part III of Form 10-K. This Amendment is also being filed to amend Item 15 of Part IV of Form 10-K to reflect the
filing of additional exhibits and the certifications required by Rule 13a-14(a) under the
Securities Exchange Act of 1934, as amended Except for the inclusion of the information described above, this Amendment does not reflect events occurring after the filing of the original Annual Report on Form
10-K on March 17, 2005 or modify or update other information or
exhibits to the Annual Report on Form
10-K.




TABLE OF CONTENTS  PART IIIItem 10. Directors and Executive Officers of the RegistrantItem 11. Executive CompensationItem 12. Security Ownership of Certain Beneficial Owners and Management and Related            Stockholder MattersItem 13. Certain Relationships and Related TransactionsItem 14. Principal Accountant Fees and ServicesPART IVITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULESSIGNATURESExhibit IndexEx-10.37 Summary of 2005 Bonus PlanEx-31.3 Certification of Chief Executive OfficerEx-31.4 Certification of Chief Financial Officer    Table of Contents  
 PART III 
 Item 10. Directors and Executive Officers of the Registrant Directors, Executive Officers and Key Employees The following table sets forth information relating to the individuals who serve as our
directors, executive officers and key employees as of April 15, 2005: Name
    
    Age
    
    PositionJean-Pierre Sommadossi, Ph.D.
    
    49
    
    President and Chief Executive Officer and Chairman of the Board of DirectorsCharlene Barshefsky
    
    54
    
    DirectorCharles W. Cramb(1)(2)
    
    58
    
    DirectorThomas Ebeling(2)
    
    46
    
    DirectorAnsbert Gadicke, M.D.
    
    47
    
    Director and Vice Chairman of the Board of DirectorsWayne T. Hockmeyer, Ph.D.(1)(2)(3)
    
    60
    
    DirectorThomas R. Hodgson(1)(2)
    
    63
    
    DirectorRobert E. Pelzer(3)
    
    51
    
    DirectorDenise Pollard-Knight, Ph.D.
    
    45
    
    DirectorDavid A. Arkowitz
    
    43
    
    Chief Financial Officer and TreasurerGuy Macdonald
    
    46
    
    Executive Vice President, OperationsNathaniel A. Brown, M.D.
    
    57
    
    Chief Medical Officer, Executive  Vice President, Hepatitis Clinical ResearchAndrea J. Corcoran
    
    42
    
    Executive Vice President, Legal and
Administration, and SecretaryJames J. Egan
    
    54
    
    Senior Vice President, Business and Corporate DevelopmentJean-Marc Allaire, M.D.
    
    44
    
    Vice President, European AffairsScot M. Barry
    
    38
    
    Vice President, ManufacturingDavid Blanchard
    
    50
    
    Vice President, Financial Planning
and AnalysisGeorge C. Chao, Ph.D.
    
    63
    
    Vice President, Biostatistics and Data ManagementPaul J. Fanning
    
    47
    
    Vice President, Human ResourcesDavid J. Franklin
    
    38
    
    Vice President, Commercial OperationsDavid A. Hallinan, Ph.D.
    
    51
    
    Vice President, Regulatory AffairsR. Christian Moreton, Ph.D.
    
    56
    
    Vice President, Pharmaceutical SciencesDavid N. Standring, Ph.D.
    
    54
    
    Vice President, BiologyRichard Storer, Ph.D.
    
    57
    
    Vice President, ChemistryDereck Tait, M.D.
    
    46
    
    Vice President, Clinical Research
 2




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(1)
    
    Member of Audit Committee(2)
    
    Member of Compensation Committee(3)
    
    Member of Nominating and Corporate Governance Committee Jean-Pierre Sommadossi, Ph.D.is the principal founder of Idenix and has served as
the chairman of our board of directors since our inception in 1998 and as our president and chief
executive officer since November 2000. During the period from November 1999 to November 2000, Dr.
Sommadossi served as our executive president and chief scientific officer. Prior to taking a
sabbatical and then unpaid leave from November 1999 to November 2002, Dr. Sommadossi served as a
professor of pharmacology, toxicology and

clinical pharmacology and associate director of both the Center for AIDS Research and the
Liver Center, University of Alabama at Birmingham School of Medicine from June 1992 to November
2000. From 1996 to 1999, Dr. Sommadossi served on the Research Agenda Committee of the AIDS
Clinical Trial Group. Dr. Sommadossi holds a Pharm.D. and Ph.D. in Pharmacology from the University
of Marseilles in France. Ambassador Charlene Barshefskyhas served as a director since June 2002. Ambassador Barshefsky
joined the law firm of Wilmer Cutler Pickering in September 2001, where she is a senior
international partner. Wilmer Cutler Pickering merged with Hale and Dorr LLP, counsel to us, in May
2004. From 1997 to 2001, Ambassador Barshefsky was the U.S. Trade Representative and served as a
member of the Cabinet of former President Clinton, as the Presidents principal trade policy
advisor and as chief trade negotiator for the U.S. Prior to that time, Ambassador Barshefsky was a
partner at the law firm of Steptoe & Johnson. In addition to her
service on our board of directors, Ambassador Barshefsky is a director of the American Express Company, The Estée Lauder
Companies Inc., Starwood Hotels & Resorts Worldwide, Inc. and Intel Corporation. Ambassador
Barshefsky holds a B.A. from the University of Wisconsin and a J.D. from the Columbus School of Law
at the Catholic University in Washington D.C. Charles W. Crambhas served as a director since October 2003. Mr. Cramb has served as the
chief financial officer of The Gillette Company, a worldwide consumer products company, since July
1997. From July 1995 to July 1997, Mr. Cramb served as a corporate vice president and corporate
controller of The Gillette Company. Mr. Cramb is a director and vice chairman of the Private Sector
Council. He is also a member of the board of directors of Tenneco Automotive Inc. Mr. Cramb holds a
B.A. from Dartmouth College and an M.B.A. from the University of Chicago. Thomas Ebelinghas served as a director since May 2003. Mr. Ebeling joined the Novartis Group,
a multinational group of companies specializing in the research, development, manufacture, sale and
distribution of innovative healthcare products, in January 1998 as chief executive officer of
Novartis Nutrition World Wide. After having served as chief executive officer of Novartis global
nutrition operations, he became chief executive officer of Novartis Consumer Health World Wide, and
then chief operating officer of the Novartis Pharmaceuticals Division. Mr. Ebeling was appointed
chief executive officer of Novartis Pharmaceuticals Division in July 2000. Prior to joining
Novartis, Mr. Ebeling served as general manager of Pepsi-Cola Germany, where he began his career in
1991 as marketing manager. Prior to working for Pepsi-Cola, Mr. Ebeling held several positions at
Reemstma Germany from 1987 to 1991. Mr. Ebeling holds a degree in psychology from the University of
Hamburg, Hamburg, Germany. Ansbert Gadicke, M.D.has served as a director since our inception in 1998. Since founding
Medical Portfolio Management, LLC, or MPM, an investment management business specializing in the
healthcare industry, in January 1992, Dr. Gadicke has served as chairman of its board of directors
and president. Dr. Gadicke also serves as a member of the board
of directors of Viacell, Inc. and various privately
held companies. Prior to founding MPM, Dr. Gadicke was employed by the Boston Consulting Group. Dr.
Gadicke has held research positions at the Whitehead Institute at Massachusetts Institute of
Technology, Harvard University and the German Cancer Research Center. Dr. Gadicke holds an M.D.
from J.W. Goethe University, Frankfurt, Germany. Wayne T. Hockmeyer, Ph.D.has served as a director since February 2002. Dr. Hockmeyer founded
MedImmune, Inc., a biotechnology company, in April 1988 and served until October 2000 as the chief
executive officer of MedImmune. In October 2000, Dr. Hockmeyer relinquished his position as chief
executive officer and now serves as chairman of the board of directors, MedImmune, Inc. and
president of MedImmune Ventures, Inc., a wholly-owned subsidiary of MedImmune, Inc. Dr. Hockmeyer
also serves as a director of Advancis Pharmaceutical Corporation,
GenVec, Inc., and TolerRx, Inc. Dr. Hockmeyer was recognized, in 1998, by the University of Florida as a
Distinguished Alumnus and in 2002 was awarded a Doctor of Science honoris causa from Purdue
University. Dr. Hockmeyer holds a B.S. from Purdue University and a Ph.D. from the University of
Florida. 3




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Thomas R. Hodgsonhas served as a director since February 2002. Since January 1999, Mr.
Hodgson has engaged in private investing activities. From September 1990 to January 1999, Mr.
Hodgson served as the president and chief operating officer of Abbott Laboratories. From 1983 to
1990, Mr. Hodgson served as the president of Abbott International and from 1978 to 1983, Mr.
Hodgson served as the president of the Hospital Products Division of Abbott Laboratories. Mr.
Hodgson is a director of The St. Paul Travelers Inc. and Intermune, Inc. Mr. Hodgson holds a B.S.
from Purdue University, an M.S. from the University of Michigan, an M.B.A. from Harvard Business
School and an honorary doctorate degree in engineering awarded by Purdue University. Robert Pelzerhas served as a director since May 2003. Mr. Pelzer is general counsel of
Novartis Pharmaceuticals Division. Prior to this appointment at Novartis in March 2002, Mr. Pelzer
was general counsel at DuPont Pharmaceuticals Company from 1998 to December 2001. Prior to that
time, Mr. Pelzer held various positions with The DuPont Company. Mr. Pelzer started his legal
career at the law firm of MacKimmie Matthews in Calgary, Alberta. Mr. Pelzer holds degrees in
Commerce and in Law from the University of Alberta. He is admitted as Barrister and Solicitor in
the Province of Alberta, Canada, and as Solicitor in England and Wales. Denise Pollard-Knight, Ph.D.has served as a director since May 2003. Since April 2004, Dr. Pollard-Knight has served as
head of Nomura Phase4 Ventures, an affiliate of Nomura International plc. From January 1999 to
March 2004, Dr. Pollard-Knight served as head of Healthcare Private Equity at Nomura International
plc, a leading Japanese financial institution. Prior to joining
Nomura, Dr. Pollard-Knight was a member of Rothschild Asset Management Ltd., an investment management
firm, from January 1997 to January 1999.
Dr. Pollard-Knight is also a director of Viacell, Inc. and
several privately held companies. Dr. Pollard-Knight held several research and development
management positions at Amersham-Pharmacia and Fisons plc. Dr. Pollard-Knight holds a Ph.D. and BSc
(Hons) from the University of Birmingham in England. Dr. Pollard-Knight completed postdoctorate
work as a Fulbright Scholar at the University of California, Berkeley. David A. Arkowitzhas served as our chief financial officer since December 2003 and as
treasurer since January 2004. Prior to joining Idenix, Mr. Arkowitz was with Merck & Co., Inc., a
pharmaceutical company, where he served as vice president and controller of the U.S. sales and
marketing division from September 2002 to December 2003, controller of the global research and
development division from April 2000 to September 2002, and as vice president finance and business
development of Mercks Canadian subsidiary from July 1997 to April 2000. Mr. Arkowitz holds an M.B.A.
from Columbia University and a B.A. from Brandeis University. Guy Macdonaldhas served as executive vice president, operations since September 2003. Prior
to joining Idenix, Mr. Macdonald was with Merck & Co., Inc., a pharmaceutical company, from
November 1981 to August 2003, most recently as vice president, anti-infectives. During his tenure
at Merck, Mr. Macdonald directed the launch of five anti-infective products and led global business
strategy for Mercks HIV franchise. Mr. Macdonald holds a B.S. from the University of Dundee,
Scotland. Nathaniel Brown, M.D.has served as our chief medical officer since September 2003 and as our
executive vice president, clinical research since September 2004, previously serving as our senior
vice president, hepatitis clinical research from January 2001 to September 2004. From September
1994 to January 2001, Dr. Brown served as principal clinical program head, hepatitis clinical
research and as director, clinical and scientific affairs for GlaxoSmithKline plc, a pharmaceutical
company. Dr. Brown served as section head, opportunistic infections for Burroughs Wellcome Co., a
pharmaceutical company, from May 1989 to September 1994. Dr. Brown was the first recipient of the
Hepatitis B Foundations Distinguished Leadership Award in 1997. He has held appointments as
assistant professor at UCLA School of Medicine and associate professor at Cornell University
Medical College. Dr. Brown holds an M.D. from Georgetown University School of Medicine and
completed post-graduate clinical and research training at The New York Hospital-Cornell Medical
Center and Yale University School of Medicine. Andrea J. Corcoranhas served as our executive vice president, legal and administration, since
February 2004 and as senior vice president, legal and administration from June 2001 until February
2004. From September 2000 until May 2003, Ms. Corcoran served as a director. Ms. Corcoran has
served as our secretary since May 2000. From December 1999 to June 2001, Ms. Corcoran served as our
vice president, legal and administration, and from December 1998 to December 1999 as our general
counsel and administration. Prior to joining Idenix, Ms. Corcoran was associated with the law firm
Kelley Drye & Warren LLP from June 1996 to September 1998 and with the law firm Edwards & Angell
LLP from July 1990 to June 1996. Ms. Corcoran holds a J.D. from Boston College Law School and a
B.S. from Providence College. James J. Eganhas served as our senior vice president, business and corporate development
since June 2001. From April 2000 to June 2001, Mr. Egan served as a consultant to us. From June
2000 to June 2001, Mr. Egan served as chief executive officer of NeuronZ Limited, a biomedical
company. From October 1993 to June 2000, Mr. Egan served as senior director, global licensing,
business development, mergers and acquisitions with G.D. Searle & Co., a subsidiary of Monsanto
Company, a life sciences company. Before joining G.D. Searle, Mr. Egan was division counsel,
international operations at Abbott Laboratories, a pharmaceutical company. Mr. Egan holds a J.D.
from the University of Santa Clara School of Law and a B.S. from Georgetown University. Jean-Marc Allaire, M.D.has served as our vice president, European operations since November
2002, and he served as senior 4




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director, European operations from October 2000 to November 2002.
Prior to joining Idenix, Dr. Allaire served as science and technology attaché at the embassy of
France in Washington D.C. from September 1999 to September 2000. From 1995 to 1999, Dr. Allaire
served as the therapeutic division director, clinical research at the Institut de Recherche Pierre
Fabre in Paris, France. Dr. Allaire holds an M.D. from the Medical School of Paris, Paris, France
and completed additional graduate work at the Institut Pasteur in Paris, France. Scot M. Barryhas served as our vice president, manufacturing since March 2002. From June 2001
to February 2002, Mr. Barry served as our senior director, pharmaceutics. Prior to joining Idenix,
Mr. Barry served from January 2001 to June 2001 as director of business development and as a
business development manager from June 2000 to December 2000 at Ricerca Biosciences, LLC, a drug
manufacturing company. Mr. Barry previously served as a scientific advisor, process development and
production from June 1998 to June 2000 and as a pilot plant production supervisor from January 1994
to June 1998 at Pharm-Eco Laboratories, Inc., a drug manufacturing company. Mr. Barry holds an M.S.
from the University of Massachusetts-Amherst and a B.S. from Southeastern Massachusetts University. David
Blanchardhas served as our vice president, financial
planning and analysis since December 2004. From
September 2004 to December 2004, Mr. Blanchard served as our executive director, financial planning
and analysis, and from December 2000 to September 2004,
as our corporate controller. Prior to joining Idenix, Mr. Blanchard served as controller for
Hope Webbing Company, a privately held fabric manufacturer, from 1998 to 2000. Mr. Blanchard
previously served as manager of budgets and forecast at The Foxboro Company from 1996 to 1998.
Mr. Blanchard holds an M.B.A. and BSBA from Nichols College. George C. Chao, Ph.D.has served as our vice president, biostatistics and data management
since January 2002. Prior to joining Idenix, Dr. Chao served as vice president, biometrics and data
management at DuPont Pharmaceuticals, Inc., a pharmaceutical company, from December 1984 to
December 2001. Dr. Chao holds a Ph.D. in Statistics and an M.S. in Experimental Statistics from
North Carolina State University and a B.S. in Agricultural Engineering from the National Taiwan
University. Paul J. Fanninghas served as our vice president, human resources since March 2004. Prior to
joining Idenix, Mr. Fanning was employed by The Foxboro Company and its affiliates from 1984 to
2004, most recently as vice president, human resources at Invensys Process Systems from 2000 to
2004 and from 1998 to 2000 as vice president, human resources, Invensys Process Automation. Mr.
Fanning holds an M.B.A. from Babson College and a B.S. from the University of Massachusetts. David J. Franklinhas served as our vice president, commercial operations since September
2001. Mr. Franklin has held positions of increasing responsibility since joining Idenix in 1998.
Prior to joining Idenix, Mr. Franklin served as product manager, and sales analysis manager for HIV
Products for Bristol-Myers Squibb Company, a pharmaceutical and related healthcare products
company, from December 1991 to September 1998. Mr. Franklin holds a B.A. from Gettysburg College. David A. Hallinan, Ph.D.has served as our vice president, regulatory affairs since September
2000. From February 1993 to August 2000, Dr. Hallinan served in several capacities, most recently
as vice president, worldwide regulatory affairs department at Parexel International Corporation, a
contract pharmaceutical outsourcing organization. From May 1990 to November 1992, Dr. Hallinan
served as associate director, regulatory affairs at G.H. Besselaar Associates, a contract
pharmaceutical research company. Dr. Hallinan holds a Ph.D. in Pharmacology from University
College, Dublin, Ireland. R. Christian Moreton, Ph.D.has served as our vice president, pharmaceutical sciences since
August 2002. Prior to joining Idenix, Dr. Moreton served as vice president, research and
development at Genpharm Inc. from May 2001 to February 2002. Prior to that time, he was with
Penwest Pharmaceuticals Co. from February 1995 until May 2002, most recently as the senior director
of technical operations. Dr. Moreton holds a B.A. in Pharmaceuticals from the University of
Nottingham and an M.S. in Pharmaceutical Analysis from the University of Strathclyde and a Ph.D.
from the University of Wales. David N. Standring, Ph.D.has served as our vice president, biology since March 2002 and he
served as our executive director of biology from September 2000 to March 2002. Prior to joining
Idenix, Dr. Standring served from July 1999 to June 2000 as associate director, and from February
1998 to July 2000, Dr. Standring served as research fellow and then as associate director, virology
department at Schering-Plough Research Institute, a division of Schering Plough Corporation, a
pharmaceutical company. From November 1994 to January 1998, Dr. Standring served as group leader,
hepatitis, virology department at Bristol-Myers Squibb Research Institute. From 1984 to 1994, Dr.
Standring was on the faculty of the University of California at San Francisco. Dr. Standring holds
a B.S. from St. Johns College, Oxford University and a Ph.D. in Bioorganic Chemistry from Harvard
University. Richard Storer, Ph.D.has served as our vice president, chemistry since March 2002. From
November 2001 to March 2002, Dr. Storer served as our executive director, chemistry. Prior to
joining Idenix, Dr. Storer served as director of chemistry at BioChem Pharma Inc., a
biopharmaceutical company, from August 1997 to August 2001. From 1996 to 1997, Dr. Storer served as
head of the combinatorial medicinal chemistry research unit and as research manager from 1988 to
1996 at GlaxoWellcome, a pharmaceutical 5




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company. Dr. Storer is a co-recipient of the 1996 Canadian
Prix Galien for the discovery of 3TC. Dr. Storer is a visiting professor at the University of
Sussex and a fellow of the Royal Society of Chemistry (U.K.). Dr. Storer holds a Ph.D. in Synthetic
Organic Chemistry from the University of Sussex and a B.S. from the University of Sussex. Dereck Tait, M.D. has served as our vice president, clinical research since October 2004.
Prior to joining Idenix, Dr. Tait served as clinical director at GlaxoSmithKline plc from December
2001 to October 2004 and as medical adviser and senior clinical program head from February 1995 to
December 2001. Dr. Tait obtained his medical qualifications from the University of Pretoria,
Pretoria, South Africa and has held postgraduate posts in clinical virology at the Royal
Postgraduate Medical School at Hammersmith Hospital, London, UK and at the University of Natal at
King Edward VIII Hospital in South Africa. There
are no family relationships among any of our directors or executive officers. Each of our executive officers devotes his or her
full time to our affairs. Each of our executive officers, other than our chief financial officer, is elected or
appointed by, and serves at the discretion of, the board of directors. Until such time as Novartis
and its affiliates own less than 50% of our voting stock, Novartis consent is required for the
selection and appointment of our chief financial officer. If in Novartis reasonable judgment our
chief financial officer is not satisfactorily performing his duties, we are required to terminate
the employment of our chief financial officer. Stockholders Agreement Pursuant to the terms of our amended and restated stockholders agreement, dated as of July
27, 2004, among us, Novartis and certain of our stockholders, we are obligated 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. In addition, the stockholders agreement further provides that for so
long as any designee of Novartis serves on our board of directors, a Novartis director designee is
entitled to be a member of each committee of our board of directors. If such membership is barred
by applicable law, rule or regulation, Novartis is entitled to designate one non-voting
observer to any such committee. For a description of our relationship with Novartis and a more detailed description
of the terms of the stockholders agreement, please refer to
Business  Collaborations  Relationship
with Novartis included in our Annual Report on Form 10-K
filed with the SEC on March 17, 2005. Section 16(a) Beneficial Ownership Reporting Compliance Section 16(a) of the Securities Exchange Act of 1934, as amended, or Exchange Act, requires
our directors, executive officers and holders of more than 10% of our common stock to file with the
Securities and Exchange Commission initial reports of ownership and reports of changes in ownership
of common stock and other of our equity securities. Based solely on our review of copies of Section
16(a) reports provided to us by the persons required to file such reports and written
representations made to us by such persons, we believe that during 2004 all filings required to be
made by our officers, directors and holders of more than 10% of our common stock were timely made
in accordance with the Section 16(a) filing requirements. Code of Ethics We have adopted a written code of business conduct and ethics that applies to our principal
executive officer, principal financial officer, principal accounting officer or persons performing
similar functions. We have posted to our website our code of business conduct and ethics. We
intend to disclose any amendments to, or waivers from, the code on our website, which is located at
www.idenix.com. Audit Committee The Audit Committee of our Board currently consists of Dr. Hockmeyer and Messrs. Cramb and
Hodgson. The Board has determined that each member of the Audit Committee is independent as
defined under the rules of the Nasdaq Stock Market, including the independence requirements
contemplated by Rule 10A-3 under the Exchange Act. The Board has also determined that Mr. Cramb is
an audit committee financial expert as defined in Item 401(h) of Regulation S-K. 6




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Item 11. Executive Compensation Compensation of Directors Our non-employee directors receive a combination of cash and equity compensation for their
service on our board of directors. In addition, members of our board are also eligible for reimbursement of
expenses incurred in connection with attendance at board and committee meetings and related
activities in accordance with Idenix policy. Our employee directors do not receive any additional
remuneration for their service on our board. None of Drs. Pollard-Knight or Gadicke or our directors who are employees of Novartis and its
affiliates, namely Messrs. Ebeling and Pelzer, receive any cash or equity compensation for service
on our board or any of its committees. Additionally, directors affiliated with Novartis are not
reimbursed for any expenses incurred in connection with their service on our board of directors. The following table describes Idenixs compensation practices for non-employee directors,
other than the non-employee directors noted above, during 2004 and 2005: Non-Employee Director CompensationOptions to purchase common stock (1)Year
    
    Cash Retainer
    
    Initial
     
    AnnualBoard Member
    2005
    
    $
    30,000
    
    
    15,000
    (2)
    
    
    20,000
    (3)2004
    
    
    30,000
    
    
    20,000
    (4)
    
    
    10,000
    (5)Committee Chair
    2005
    
    
    5,000
    
    
    
    
    
    
    2004
    
    
    5,000
    
    
    
    
    
    
    
   (1)
    
    The exercise price of these options is equal to the fair market value of our common
stock on the date of grant as reported by NASDAQ. Each option terminates on the earlier of
ten years from the date of grant or 90 days after the optionee ceases to serve as a
director, except in the case of death or disability, in which event the option terminates
one year from the date of the directors death or disability.(2)
    
    Each non-employee director is entitled to receive an award of stock options upon
his or her election or appointment to our board of directors. The number of options to be
awarded to new directors who are appointed to the Board at times other than immediately
after the annual meeting of stockholders will be prorated for the period of service between
date of appointment and the annual meeting. The options vest in 12 monthly equal
installments from the date of grant.(3)
    
    Each non-employee director is entitled to receive at each years annual meeting after
which he or she continues to serve as a director, an additional option grant of 10,000
shares. The annual option grant vests in 12 equal monthly installments from the date of
grant.(4)
    
    No initial option grants were made in 2004. 7




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(5)
    
    The annual grant was awarded only to Mr. Cramb who began his service as a director in
2003. Our other non-employee directors, Ambassador Barshefsky, Dr. Hockmeyer and Mr.
Hodgson, each of whom began their service as directors prior to 2003 were not entitled to
receive annual equity awards until their third anniversary of service commencement. Executive Compensation The
following table shows, for the years ended December 31, 2004,
2003 and 2002, the
compensation awarded or paid to, or earned by, our Chief Executive Officer and our other most
highly compensated executive officers and one former executive officer. We refer to this group as
our named executive officers. Summary Compensation Table Long TermAnnual Compensation
    
    
    CompensationSharesYear Ended
    
    
    
    
    
    
    
    
    
    
    Other Annual
    
    
    Underlying
    
    
    All OtherName and Principal Position
    
    December 31,
    
    
    Salary
    
    
    Bonus(1)
    
    
    Compensation
    
    

Options($)(2)
    
    
    CompensationJean-Pierre Sommadossi
    
    
    2004
    
    
    $
    421,383
    
    
    $
    225,000
    
    
    $
    64,694
    (3)
    
    
    100,000
    
    
    
    Chairman of
the Board of Directors,
    
    
    2003
    
    
    
    381,600
    
    
    
    600,000
    (4)
    
    
    
    
    
    
    
    
    
    
    President
and Chief
    
    
    2002
    
    
    
    323,500
    
    
    
    150,000
    
    
    
    131,450
    (3)
    
    
    100,000
    
    
    
    Executive Officer
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    100,000
    
    
    
    David A. Arkowitz (5)
    
    
    2004
    
    
    
    290,000
    
    
    
    120,000
    
    
    
    62,937
    (3)
    
    
    30,000
    
    
    
    Chief Financial Officer and
    
    
    2003
    
    
    
    18,528
    
    
    
    200,000
    (6)
    
    
    
    
    
    
    
    
    
    
    Treasurer
    
    
    2002
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    175,000
    
    
    
    Nathaniel A. Brown
    
    
    2004
    
    
    
    260,836
    
    
    
    100,000
    
    
    
    21,439
    (7)
    
    
    30,000
    
    
    
    Executive
Vice President, Clinical
    
    
    2003
    
    
    
    251,114
    
    
    
    80,000
    
    
    
    21,346
    (7)
    
    
    
    
    
    
    Research, and Chief Medical
Officer
    
    
    2002
    
    
    
    238,084
    
    
    
    
    
    
    
    20,991
    (7)
    
    
    5,000
    
    
    
    Guy Macdonald (8)
    
    
    2004
    
    
    
    290,000
    
    
    
    110,000
    
    
    
    27,685
    (3)
    
    
    30,000
    
    
    
    3,442
    (9)Executive Vice
    
    
    2003
    
    
    
    95,861
    
    
    
    300,000
    (10)
    
    
    31,853
    (3)
    
    
    175,000President,
    
    
    2002
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Andrea J. Corcoran
    
    
    2004
    
    
    
    257,400
    
    
    
    85,000
    
    
    
    
    
    
    
    30,000
    
    
    
    Executive Vice President, Legal
and
    
    
    2003
    
    
    
    228,795
    
    
    
    100,000
    
    
    
    
    
    
    
    
    
    
    
    Administration,
and Secretary
    
    
    2002
    
    
    
    216,923
    
    
    
    
    
    
    
    
    
    
    
    5,000
    
    
    
    David M. Shlaes (11)
    
    
    2004
    
    
    
    263,000
    
    
    
    131,666
    (12)
    
    
    
    
    
    
    30,000
    
    
    
    Senior Fellow
    
    
    2003
    
    
    
    275,600
    
    
    
    85,000
    
    
    
    
    
    
    
    
    
    
    
    2002
    
    
    
    144,300
    
    
    
    76,667
    
    
    
    92,685
    (3)
    
    
    230,000
    
    
    
    
   (1)
    
    Bonus amounts for the year indicated are paid in February of the
immediately following year. Amounts paid are determined based on the Compensation Committees
review of corporate performance and individual achievements for the relevant year.(2)
    
    We have not granted any stock appreciation rights, made any long-term
incentive plan awards or made any restricted stock grants to any executive officer, including
the named executive officers, or any other employee during the periods covered.(3)
    
    Represents amounts paid for reimbursement of relocation expenses, including amounts required
to be paid to gross up such expenses for tax purposes.(4)
    
    Includes $400,000 bonus received upon consummation of our collaboration with Novartis.(5)
    
    Mr. Arkowitz became an executive officer in December 2003.(6)
    
    Consists of $200,000 sign-on bonus.(7)
    
    Represents forgiveness of principal and interest on $60,000 relocation loan.(8)
    
    Mr. Macdonald became an executive officer in September 2003. 8




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##### Table of Contents



(9)
    
    Represents supplemental life insurance premium paid by the company.(10)
    
    Includes $200,000 sign-on bonus.(11)
    
    Dr. Shlaes resigned from his position as an executive officer effective November 2,
2004.(12)
    
    Includes current year installment in the amount of $66,667 of sign-on bonus awarded at
employment commencement. Stock Option Grants and Exercises In 2004, we granted both incentive stock options and nonstatutory stock options to our
officers. The following tables show, for the year ended December 31, 2004, certain
information regarding options granted to, exercised by, and held at
year-end by our named executive
officers: Option Grants in Last Fiscal Year Individual Grants% of Total
    
    
    
    
    
    
    
    
    
    
    Potential Realizable ValueShares
    
    
    Options
    
    
    
    
    
    
    
    
    
    
    at Assumed Annual Rates ofUnderlying
    
    
    Granted to
    
    
    Exercise
    
    
    
    
    
    
    Stock Price AppreciationOptions
    
    
    Employees in
    
    
    Price Per
    
    
    Expiration
    
    
    for Option Term(4)Name
    
    Granted(1)
    
    
    2004(2)
    
    
    Share(3)
    
    
    Date
    
    
    5%
    
    
    10%Jena-Pierre Sommadossi
    
    
    100,000
    
    
    
    10.74
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    757,818
    
    
    $
    1,920,460David A. Arkowitz
    
    
    30,000
    
    
    
    3.22
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    227,345
    
    
    $
    576,138Nathaniel A. Brown
    
    
    30,000
    
    
    
    3.22
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    227,345
    
    
    $
    576,138Guy Macdonald
    
    
    30,000
    
    
    
    3.22
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    227,345
    
    
    $
    576,138Andrea J. Corcoran
    
    
    30,000
    
    
    
    3.22
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    227,345
    
    
    $
    576,138David M. Shlaes
    
    
    30,000
    
    
    
    3.22
    %
    
    $
    12.05
    
    
    
    2/01/14
    
    
    $
    227,345
    
    
    $
    576,138
   (1)
    
    The terms of such options, which were granted in February 2004, are substantially
consistent with those of options granted to other employees under the Idenix
Pharmaceuticals, Inc. 1998 Equity Incentive Plan, as amended, which
we refer to as our 1998
Plan. The options were immediately exercisable for restricted stock. For all persons
other than Dr. Sommadossi, our right of repurchase and other restrictions lapse ratably
over a period of 48 successive months beginning in the month of option grant. For Dr.
Sommadossi, our right of repurchase and other restrictions lapse with respect to 25% of the
total award on the first anniversary of option grant and with respect to the remaining 75%
of the total award over a period of 48 successive months.(2)
    
    Based on options to purchase 930,900 shares of common stock granted to employees,
including executive officers, for the year ended December 31, 2004.(3)
    
    The exercise price per share represents the fair market value of our common stock on
the grant date as reported by NASDAQ.(4)
    
    The potential realizable value is based on the term of the option at the date of the
grant, which is ten years. It is calculated by assuming that the stock price on the date of
grant appreciates at the indicated annual rate, compounded annually for the entire term,
and that the option is exercised and sold on the last day of the option term for the
appreciated stock price. Actual gains, if any, are dependent on the actual future
performance of our common stock and the timing of exercise and sale transactions by the
holder. These numbers are based on the SEC requirements and do not reflect our projection
or estimate of future stock price growth.


9



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Aggregated Option Exercises in Last Fiscal Year and Fiscal Year-End Option Values Shares of Common StockUnderlying Unexercised
    
    
    Value of UnexercisedShares
    
    
    
    
    
    
    Options at
    
    
    In-the-Money Options atAcquired
    
    
    Value
    
    
    December 31, 2004(2)
    
    
    December 31, 2004(3)on Exercise
    
    
    Realized(1)
    
    
    Exercisable
    
    
    Unexercisable
    
    
    Exercisable
    
    
    UnexercisableJean-Pierre Sommadossi
    
    
    43,750
    
    
    $
    161,875
    
    
    
    10,417
    
    
    
    145,833
    
    
    $
    91,670
    
    
    $
    928,330David A. Arkowitz
    
    
    
    
    
    $
    
    
    
    
    54,271
    
    
    
    150,729
    
    
    $
    310,991
    
    
    $
    861,509Nathaniel A. Brown
    
    
    
    
    
    $
    
    
    
    
    126,458
    
    
    
    70,417
    
    
    $
    1,848,112
    
    
    $
    830,076Guy Macdonald
    
    
    
    
    
    $
    
    
    
    
    65,208
    
    
    
    139,792
    
    
    $
    374,425
    
    
    $
    798,075Andrea J. Corcoran
    
    
    
    
    
    $
    
    
    
    
    95,292
    
    
    
    38,021
    
    
    $
    1,373,167
    
    
    $
    252,491David M. Shlaes
    
    
    
    
    
    $
    
    
    
    
    111,645
    
    
    
    137,917
    
    
    $
    1,519,411
    
    
    $
    1,750,326
   (1)
    
    Represents the aggregate fair value of the shares of our
common stock acquired (based on the average open and close price
reported on the dates of exercise by NASDAQ less the exercise price).(2)
    
    Each of these options is immediately exercisable on the date of grant for shares of
restricted common stock which are subject to vesting over time. The term exercisable in
this column reflects such portion of the option that, if exercised, would be exercisable
for fully vested shares.(3)
    
    Represents the fair value of the option based on the fair value of Idenixs common
stock at December 31, 2004 ($17.30 based on the average open and
close price reported by NASDAQ), less the exercise price. Employment Agreements We have entered into employment agreements with each of Drs. Sommadossi and Brown, Messrs.
Arkowitz and Macdonald and Ms. Corcoran. The terms of employment under these agreements, subject to earlier termination, runs to May
2008 for Drs. Sommadossi and Brown and Ms. Corcoran and to September and December 2006,
respectively, for Messrs. Macdonald and Arkowitz. The agreements are automatically renewable
after the initial term for successive one-year periods unless either party gives written notice to
the other 90 days, or in the case of Mr. Arkowitz
120 days prior to the expiration of the term. The employment agreements for each officer provide base salary in an amount annually
reviewable for increase, but not decrease, at the discretion of our board of directors or a
committee of the board of directors. The employment agreements also entitle each officer to
receive an annual cash performance bonus in an amount that is expressed as percentage of base
salary if the board of directors in its discretion determines that such officer has achieved or
surpassed performance goals established by the board of directors in consultation with our
management. The minimum target bonus percentages for each officer are set forth in each officers
employment agreement. For Dr. Sommadossi, the minimum target percentage is 40% of base salary and
for each other officer the minimum target percentage is 30% of base salary. Each officer is also
eligible to participate in any of our equity incentive programs and has the opportunity, subject to
approval of the board of directors, to be awarded annually an option to purchase shares of our
common stock which vest over a four year period (except for awards granted to Dr. Sommadossi which
vest over a five year period). Effective as of January 1, 2005,
the current base salaries, the
target bonus amount and target option award for 2005 are set forth
below for each named executive officer: 2005Target Bonus as a %Officer
    
    Base Salary
    
    
    of Base Salary
    
    Target Option AwardJean-Pierre Sommadossi
    
    $
475,000
    
    

60%
    
    

150,000David Arkowitz
    
    
    298,700
    
    
    40
    
    
    30,000Nathaniel Brown
    
    
    298,700
    
    
    40
    
    
    30,000Andrea Corcoran
    
    
    267,800
    
    
    35
    
    
    30,000Guy Macdonald
    
    
    298,700
    
    
    40
    
    
    30,000
 The employment agreements include provisions that are effective upon termination of the
employment of the officer in certain circumstances. In the event that we terminate an officers
employment without cause, or if the officer terminates his employment for good reason:  
    the officer is entitled to receive:  Ø
    a lump-sum severance payment equal to one times his base salary (two times his
base salary in the case of Dr. Sommadossi); andØ
    the greater of such officers current year target bonus amount or the bonus
such officer earned for the year preceding the year in which the termination
occurs; and 10




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
    all of outstanding equity awards held by the officer as of the time of termination
will become immediately vested and exercisable. Additionally, in the case of Messrs. Macdonald and Arkowitz, if we elect not to extend such
officers employment beyond its initial term, expiring in each case in 2006, the option to purchase
175,000 shares of our common stock awarded to each of Messrs. Macdonald and Arkowitz at the
commencement of his employment will become immediately vested and exercisable for a period of 15
months following the date of employment termination. In the event an officers employment terminates as described above or due to disability or
death, the officer or such officers estate, is entitled to receive a pro rata share of the
officers annual performance bonus and equity option award, continued medical, dental and life
insurance coverage for himself and eligible dependents for up to 12 months after termination (24
months in the case of Dr. Sommadossi) and all outstanding equity awards held by the officer as of
the time of such death or disability will become immediately vested and exercisable. In the event
of disability, each officer is entitled to an additional payment of 60% of his base salary per year
until he reaches age 65. Additionally, Dr. Sommadossi is entitled to life and disability insurance
benefits payable in the amount of $2 million in event of his death or disability and Mr. Macdonald
is entitled to life insurance benefits payable in the amount of $1 million in event of his death.
In the event that Mr. Arkowitz employment terminates due to death or disability, all of his
outstanding equity awards will become immediately vested and exercisable for a period of two years
following the date of employment termination. Further, in the event of employment termination as a
result of either death or the occurrence of death within 6 months after employment termination as a
result of the condition which necessitated such termination, Mr. Arkowitzs estate is entitled to a
payment equal to one-half of his termination payment. If, within one year following a change in control of Idenix, we terminate an officers
employment without cause or if such officer terminates their employment for good reason, the
officer is entitled to an additional lump-sum payment in an amount equal to:  
    such officers base salary; and
    the greater of such officers target bonus amount or the bonus earned
in the year preceding the year in which the termination occurs. We have also agreed to compensate each officer for excise taxes and associated penalties
imposed by Section 4999 of the Internal Revenue Code by paying gross-up amounts on any applicable
benefits such officer receives under their respective employment agreement. The employment agreement Drs. Sommadossi and Brown and Ms. Corcoran have entered into include
restrictive covenants prohibiting the sale, transfer or disposition of more than 50% of the Idenix
capital stock owned by such officer on May 8, 2003, plus shares of common stock such officer
acquires upon exercise of stock options outstanding as of that date, until May 8, 2008, unless:  
    the officers employment is terminated without cause;
    the officer resigns for good reason; or
    the employment termination is a result of the officers death or disability. In connection with the commencement of their employment with Idenix in 2003, each of Messrs.
Macdonald and Arkowitz received a $200,000 sign-on bonus. These sign-on bonuses are repayable in
part if the employment of such officer is terminated, in the case of Mr. Macdonald prior to
September 2, 2005, and in the case of Mr. Arkowitz, prior to December 1, 2005, other than by us
without cause, by the officer for good reason or as a result of death or disability. Additionally,
to facilitate their relocation to the Cambridge, Massachusetts area, we agreed to reimburse
both officers for their respective expenses incurred in connection with their relocation to
Massachusetts, including up to $25,000 in relocation expenses, up to 6% of real estate commissions
incurred, 90 days temporary housing, and such amounts required to gross up these expenses for tax
purposes. In 2004, for relocation expenses Mr. Macdonald was reimbursed $16,127 and Mr. Arkowitz
was reimbursed $36,985. Effective
November 2, 2004, Dr. Shlaes left the office of executive
vice president, research
and development, and became a senior fellow. Dr. Shlaes remained
a full time employee through December 31, 2004 and became a part time employee on January 1, 2005. Under the terms of
his employment agreement, Dr. Shlaes will receive an annual base salary of $200,000 during the
employment term that runs to June 30, 2005. The employment term may be extended upon mutual
agreement of the Company and Dr. Shlaes. In addition, Dr. Shlaes received a bonus in the amount of
$65,000 for services rendered in 2004. If Dr. Shlaes continues his employment until June 30, 2005,
he will also receive a payment, which is referred to as the retention bonus, in the amount of
$66,667 representing the final installment of a bonus awarded to Dr. Shlaes in 2002. 11




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If we terminate Dr. Shlaes employment without cause during the employment period, Dr. Shlaes
will be entitled to receive a lump-sum payment in an amount equal to: (i) his base salary through
the expiration of the initial employment term, (ii) the retention bonus; and (iii) the target bonus
in the amount of $82,950 or such lesser portion thereof as the board of directors in its discretion
has determined was earned. Additionally, if Dr. Shlaes employment is terminated due to death or disability or we
terminate Dr. Shlaes employment without cause during the employment period, Dr. Shlaes, or his
estate, is entitled to receive continued medical, dental and life insurance coverage for himself
and eligible dependents for up to 12 months after termination, and all of his outstanding equity
awards
which would have become vested on or prior to June 30, 2005, will become immediately vested
and exercisable. In the event of disability, Dr. Shlaes is also entitled to receive until June 30,
2005, payments aggregating 60% of his base salary. The employment agreement includes restrictive covenants prohibiting the sale, transfer or
disposition of more than 50% of the shares of Idenix common stock Dr. Shlaes may acquire upon
exercise of stock options outstanding as of May 9, 2003 until the termination of the employment
period unless: (i) we terminate Dr. Shlaes employment without cause; or (ii) the employment
termination is a result of Dr. Shlaes death or disability. Compensation Committee Interlocks and Insider Participation The members of the compensation committee of our board of directors are Dr. Hockmeyer and
Messrs. Cramb, Ebeling and Hodgson. No member of the compensation committee was at any time during
2004, or formerly, an officer or employee of Idenix or any subsidiary of Idenix. Mr. Ebeling
serves on the compensation committee as a designee of Novartis pursuant to the terms of our
stockholders agreement. No other member of the compensation committee had any relationship
with us requiring disclosure under Item 404 of Regulation S-K under the Exchange Act. None of our executive officers has served as a director or member of the compensation
committee (or other committee serving an equivalent function) of any other entity, one of whose
executive officers served as a director of or member of our compensation committee. 
 Item 12. Security Ownership of Certain Beneficial Owners and Management and Related
Stockholder Matters The following table sets forth information regarding the ownership of our common stock as
of March 31, 2005 by:  
    each of our directors and the named executive officers;
    each person or group of affiliated persons known to us to be the beneficial owners
of more than five percent of the outstanding shares of our common stock; and
    all of our executive officers and directors as a group. Beneficial ownership is determined in accordance with the rules of the SEC, and includes
voting or investment power with respect to shares of our common stock. Shares of our common stock
issuable under stock options that are exercisable within 60 days after March 31, 2005 are deemed
outstanding for computing the percentage ownership of the person holding the options or warrants
but are not deemed outstanding for computing the percentage ownership of any other person. Unless otherwise indicated in the footnotes to this table and subject to community property
laws where applicable, to our knowledge, each of the stockholders named in this table has sole
voting and investment power with respect to the shares indicated as beneficially owned. Except as
shown otherwise in the table, the address of each stockholder listed is in care of Idenix
Pharmaceuticals, Inc., 60 Hampshire Street, Cambridge, Massachusetts 02139. Shares of Common
    
    Percentage ofStock Beneficially
    
    Common StockName and Address
    
    Owned (1)
    
    Outstanding5% StockholdersNovartis AGLichtstrasse 35CH-4002 BaselSwitzerland
    
    27,356,681 (2)
    
    
    56.84
    %MPM Capital111 Huntington AvenueBoston, Massachusetts 02199
    
    4,797,991 (3)
    
    
    9.97
    %Directors
 12




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##### Table of Contents



Jean-Pierre Sommadossi
    
    2,515,104
    (4)

    5.21%Charlene Barshefsky
    
    61,343
    (5)

    *Charles W. Cramb
    
    43,033
    

    *Thomas Ebeling
    


    

    Ansbert Gadicke
    
    4,797,991
    (6)

    9.97Wayne T. Hockmeyer
    
    41,708
    

    *Thomas Hodgson
    
    42,324
    

    *Robert Pelzer
    
    
    

    Denise Pollard-Knight
    
    
    

    Other Named Executive OfficersDavid Arkowitz
    
    214,875
    

    *Nathaniel Brown, M.D.
    
    198,750
    

    *Guy Macdonald
    
    216,875
    

    *Andrea J. Corcoran
    
    198,512
    

    *David Shlaes, M.D., Ph.D.
    
    230,562
    

    *All directors and executive officers as a group (15 persons)
    
    8,584,493
    

    17.41
   *

    Represents beneficial ownership of less than one percent of common stock.  (1)
    The number of shares of common stock that each person is deemed to beneficially own
includes the number of shares of common stock that such person has the right to acquire within
60 days after March 31, 2005. The number of such shares acquirable upon exercise of
outstanding stock options is as follows: NumberName
    
    of SharesCharles W. Cramb
    
    
    35,833Jean-Pierre Sommadossi
    
    
    156,250David Arkowitz
    
    
    206,875Nathaniel Brown
    
    
    198,750Guy MacDonald
    
    
    206,875Andrea J. Corcoran
    
    
    135,188David Shlaes
    
    
    230,562All current directors and executive officers as a group (15 persons)
    
    
    1,170,333
  (2)
    Consists of 26,169,646 shares held by Novartis Pharma AG, a direct, wholly-owned
subsidiary of Novartis AG, and 1,187,093 shares held by Novartis BioVentures Ltd., an
indirect, wholly-owned subsidiary of Novartis AG. This information is based solely on
information set forth in a Schedule 13D filed on August 6, 2004 jointly by Novartis AG,
Novartis Pharma AG and Novartis BioVentures Ltd.  (3)
    Consists of 4,292,188 shares held by BB BioVentures L.P., or BB BioVentures, 373,298 shares
held by MPM Bioventures Parallel Fund L.P., or Parallel Fund, 54,277 shares held by MPM Asset
Management Investors 1998 LLC, or Investors Fund, and 78,228 shares held by MPM Asset
Management. Each of these funds is affiliated with MPM Capital. Dr. Ansbert Gadicke, vice
chairman of our board of directors, is chairman of the board and president of Medical
Portfolio Management, LLC, the general partner of MPM Capital. This information is based
solely on information set forth in a Schedule 13G filed by such entities on February 9, 2005.  (4)
    Includes 37,810 shares held by the Jean-Pierre Sommadossi 2002 Qualified Annuity Trust,
200,000 shares held by the Jean-Pierre Sommadossi 2004 Qualified Annuity Trust.  (5)
    Includes 41,343 shares held by the Charlene Barshefsky Grantor Retained Annuity Trust dated
January 30, 2004.  (6)
    Consists of 4,797,991 shares owned by MPM Capital affiliated funds. See footnote 3 above. Dr.
Ansbert Gadicke, vice chairman of our board of directors, is chairman of the board and
president of Medical Portfolio Management, LLC, the general partner of MPM Capital and, in
such capacity, Dr. Gadicke may be deemed to have beneficial ownership of 4,797,991 shares held
by MPM Capital affiliated funds. Dr. Gadicke disclaims beneficial ownership of these shares,
except to the extent of his pecuniary interest therein. 13




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##### Table of Contents



Equity Compensation Plan Information The following table provides information about the securities authorized for issuance under
our equity compensation plans as of December 31, 2004. Equity Compensation Table Number of securities remainingWeighted average
    
    available for future issuanceexercise price of
    
    under equity compensation plansNumber of securities to be issued


    
    outstanding
    
    (excluding securities reflected inPlan Category
    
    upon exercise of outstanding options


    
    options
    
    column(a))(a)


    
    (b)
    
    (c)Equity compensation plans
approved by security
holders
    
    3,161,790
(1)

    
    $7.50
    
    749,258
(2)Equity compensation plans
not approved by security
holders
    
    -0-


    
    -0-
    
    -0-Total:
    
    3,161,790


    
    
    
    749,258
   (1)
    
    Includes 3,074,040 shares of our common stock issuable upon exercise of options to
purchase common stock awarded under our 1998 Plan and 87,750
shares of common stock issuable upon exercise of options to purchase common stock awarded
under the Idenix Pharmaceuticals, Inc. 2004 Stock Incentive Plan,
which we refer to as our 2004 Stock Incentive Plan.(2)
    
    Includes 37,008 shares of our common stock issuable under our 1998 Plan and 712,250 shares of common stock issuable under our 2004 Stock
Incentive Plan. 
 Item 13. Certain Relationships and Related Transactions Agreements Relationships with Novartis We have entered into agreements with Novartis, including a development agreement, supply
agreement, stock purchase agreement and stockholders agreement. For a discussion of these agreements and related obligations
please refer to Business-Collaborations-Relationship with
Novartis included in our Annual Report
on Form 10-K filed with the SEC on March 17, 2005. 14




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##### Table of Contents



Employment Agreement James Egan We entered into an employment agreement with Mr. Egan in May 2003 with an initial term of five
years. The agreement is automatically renewable for successive one-year periods unless either party
gives written notice to the other party 90 days prior to the expiration of the term. Under the
agreement, Mr. Egan currently receives an annual base salary of $265,000, subject to increase at
the discretion of our board of directors or a subcommittee of the board of directors. In addition,
Mr. Egan is entitled to receive an annual performance bonus of not less than 30% of his base
salary, which we refer to as his target bonus amount, and not more than 200% of his target bonus
amount, to be paid at the discretion of the board of directors if he achieves or surpasses
performance goals established by the board of directors in consultation with our management. The agreement further provides that Mr. Egan is eligible to participate in any of our equity
incentive programs and shall have an opportunity, subject to the approval of our board of
directors, to be awarded annually an option to purchase 30,000 shares of our common stock which
would vest over four years. The employment agreement also provides that if we terminate Mr. Egans employment without
cause or if Mr. Egan terminates his employment for good reason, he is entitled to receive a
lump-sum payment equal to his base salary, plus the greater of:  
    his target bonus amount; or
    the bonus he earned for the year preceding the year in which the termination occurs. 15




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##### Table of Contents



Additionally, if such termination occurs as set forth above or if employment terminates due to
death or disability, Mr. Egan, or his estate, is entitled to receive continued medical, dental and
life insurance coverage for himself and eligible dependents for up to 12 months after termination,
and all of his outstanding equity awards will become immediately vested and exercisable. Mr. Egan
is also entitled to an additional payment of 60% of his base salary per year until he reaches age
65 in the event of disability. If within one
year following a change in control of Idenix, we terminate Mr. Egans employment without cause or
Mr. Egan terminates his employment for good reason, he is entitled to an additional lump-sum amount
equal to his base salary, plus the greater of:  
    his target bonus amount; or
    the bonus he earned for the year preceding the year in which the termination occurs. We also agreed to pay gross-up amounts on benefits received by Mr. Egan under this agreement to
compensate for excise taxes and associated penalties imposed by Section 4999 of the Internal
Revenue Code. In addition, the employment agreement includes restrictive covenants prohibiting the sale,
transfer or disposition of more than 50% of the Idenix capital stock Mr. Egan owned on May 8, 2003,
plus shares of common stock Mr. Egan acquires upon exercise of stock options outstanding as of that
date, until May 8, 2008, unless:  
    we terminate Mr. Egans employment without cause;
    Mr. Egan resigns for good reason; or
    the employment termination is a result of Mr. Egans death or disability. Registration Rights As
of April 15, 2005, the holders of 36,194,463 shares of our common stock are entitled to cause
us to register their shares or participate in a registration by us under the Securities Act. These
rights are provided under the terms of the stockholders agreement. These holders include the
following directors, officer and holders of more than five percent of our voting securities and
their affiliates: Number ofName of Holder
    
    Registrable SharesNovartis AG(1)
    
    27,356,681MPM Capital L.P. affiliated funds(2)
    
    4,797,991Jean-Pierre Sommadossi
    
    100,000Total
    
    32,254,672
   (1)
    
    Represents 26,169,646 shares held by Novartis, a direct, wholly-owned subsidiary of Novartis
AG, and 1,187,093 shares held by Novartis BioVentures Ltd., an indirect wholly-owned
subsidiary of Novartis AG. Mr. Ebeling, one of our directors, serves as chief executive
officer of the Novartis Pharmaceuticals Division, an affiliate of Novartis, and Mr. Pelzer,
also one of our directors, serves as general counsel to Novartis Pharmaceuticals Division. 16




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##### Table of Contents



(2)
    
    Represents 4,292,188 shares held by BB BioVentures, 373,298 shares held by Parallel Fund, and
54,277 shares held by Investors Fund. Each of these funds is affiliated with MPM Capital. Dr.
Ansbert Gadicke, vice chairman of our board of directors, is chairman of the board and
president of Medical Portfolio Management, LLC, the general partner of MPM Capital. 
 Item 14. Principal Accountant Fees and Services Auditors Fees The
following table summarizes the fees PricewaterhouseCoopers, LLP, our
independent registered public
accounting firm, billed to us for each of the last two fiscal years for audit services and for
other services: Fee Category
    
    2004
    
    
    2003Audit Fees (1)
    
    $
    442,739
    
    
    $
    319,253Audit-Related Fees(2)
    
    
    16,450
    
    
    
    11,690Tax Fees (3)
    
    
    192,035
    
    
    
    204,721All Other Fees
    
    
    
    
    
    
    Total Fees
    
    $
    649,244
    
    
    $
    535,664
   (1)
    
    Audit fees consist of fees for the audit of our financial statements, the review of the
interim financial statements included in our quarterly reports on Form 10-Q, and other
professional services provided in connection with statutory and regulatory filings or
engagements. Audit fees included $230,043 in 2004 and $122,200 in 2003 for services rendered
by our independent auditors in connection with our initial public offering.(2)
    
    Audit-related fees consist of fees for assurance and related services that are reasonably
related to the performance of the audit and the review of our financial statements and which
are not reported under Audit Fees. These services relate to consultations concerning
financial accounting and reporting standards.(3)
    
    Tax fees consist of fees for tax compliance, tax advice and tax planning services.
Tax compliance services, which relate to services provided for preparation of original and
amended tax returns, accounted for $28,505 and $82,455 of the total tax fees billed in 2004
and 2003, respectively. Tax advice and tax planning services relate to United States
federal and state and international tax planning and advice. No audit-related or tax fees billed in 2004 or 2003 were provided under the de minimis
exception to the audit committee pre-approval requirements. Pre-Approval Policies and Procedures The Audit Committee has adopted policies and procedures relating to the approval of all audit
and non-audit services that are to be performed by our independent registered public accounting firm. This
policy generally provides we will not engage our registered public accounting firm to render audit
or non-audit services unless the service is specifically approved in advance by the Audit Committee
or the engagement is entered into pursuant to one of the pre-approval procedures described below. From time to time, the Audit Committee may pre-approve specified types of services that are
expected to be provided to us by our independent registered public accounting firm during the next 12 months.
Any such pre-approval is detailed as to the particular service or type of services to be provided
and is also generally subject to a maximum dollar amount. The Audit Committee has also delegated to the chair of the Audit Committee the authority to
approve any audit or non-audit services to be provided to us by our
independent registered public accounting
firm. Any approval of services by a member of the Audit Committee pursuant to this delegated
authority is reported on at the next meeting of the Audit Committee. 
 PART IV 
 ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES 17




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##### Table of Contents



(a)
    The Exhibits filed as part of this Amendment No. 1 on Form 10-K/A are listed in
the Exhibit Index immediately preceding such exhibits, which Exhibit Index is
incorporated herein by reference. 18




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##### Table of Contents



SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934,
the registrant has duly caused this Amendment No. 1 on Form 10-K/A to the Registrants Annual
Report on Form 10-K to be signed on its behalf by the undersigned, thereunto duly authorized. IDENIX PHARMACEUTICALS, INC./s/ Jean-Pierre SommadossiJean-Pierre SommadossiDate:
May 2, 2005
    
    
    
    Chairman and Chief Executive Officer
 19




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##### Table of Contents



Exhibit Index Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number3.1
    
    Restated Certificate of
Incorporation
    
    
    
    S-1
File No. 333-111157
    
    12/15/03
    
    3.13.2
    
    Certificate of Amendment
of Restated Certificate of
Incorporation
    
    
    
    10-Q 
File No. 000-49839
    
    8/26/2004
    
    3.13.3
    
    Amended and Restated
By-Laws
    
    
    
    10-Q 
File No. 000-49839
    
    8/26/2004
    
    3.23.4
    
    Specimen Certificate
evidencing the Common
Stock, $.001 par value
    
    
    
    S-1/Amendment 2
File No. 333-111157
    
    1/27/2004
    
    4.110.1
    
    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
File No. 333-111157
    
    12/15/2003
    
    10.410.2+
    
    Restated and Amended
Cooperative Agreement
dated as of May 8, 2003,
by and among Idenix SARL
and Le Centre National de
la Recherche Scientifique,
LUniversite Montpellier
II and Novartis Pharma AG
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.14+10.3+
    
    License Agreement, dated
as of June 20, 1998, by
and among the Registrant,
TherapX Pharmaceuticals,
L.L.C. and Raymond
Schinazi.
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.15+10.4+
    
    Cooperative Antiviral
Research Activity
Agreement (the
Cooperative Agreement),
dated January 4, 1999, by
and between Idenix SARL
and the University of
Cagliari
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.16+10.5+
    
    License Agreement, dated
as of December 14, 2000,
between the Registrant and
the University of Cagliari
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.17+
 20




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Exhibit Index Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number10.6+
    
    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/Amendment 3
File No. 333-11157
    
    7/6/2004
    
    10.18+10.7+
    
    Agreement, dated June 30,
2004, by and among the
Registrant, Idenix SARL
and the University of
Cagliari
    
    
    
    S-1/Amendment 3
File No. 333-11157
    
    7/6/2004
    
    10.18.1+10.8
    
    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
File No. 333-11157
    
    7/6/2004
    
    10.18.210.9
    
    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
File No. 333-11157
    
    12/15/2003
    
    10.1910.10
    
    Master Services Agreement,
dated May 27, 1999,
between Idenix
(Massachusetts), Inc. and
Quintiles Scotland Ltd
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.2010.11+
    
    Master Services Agreement,
dated February 25, 2003,
by and between the
Registrant and Quintiles,
Inc.
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.21+10.12
    
    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
File No. 333-11157
    
    12/15/2003
    
    10.2210.13+
    
    Agreement, dated as of May
1, 2003, between Idenix
(Cayman) Limited and
Microbiologica Quimica E
Farmaceutica Ltda.
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.23+
 21




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##### Table of Contents



Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number10.14+
    
    Master Manufacturing and
Supply Agreement, dated as
of May 8, 2003, by and
between Idenix (Cayman)
Limited and Novartis
Pharma AG.
    
    
    
    S-1
File No. 333-11157
    
    12/15/2003
    
    10.25+10.15+
    
    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- S-1/Amendment 3
File No. 333-11157
    
    7/6/2004
    
    10.24+10.16+
    
    Second Amendment, dated as
of December 21, 2004, to
the Development, License
and Commercialization
Agreement, by and among
the Registrant, Idenix
(Cayman) Limited and
Novartis Pharma AG, as
amended on April 30, 2004
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.1610.17
    
    Letter Agreement, dated as
of March 21, 2003, by and
between the Registrant and
Novartis Pharma AG.
    
    
    
    S-1/Amendment 3
File No. 333-111157
    
    7/6/2004
    
    10.2810.18+
    
    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
File No. 333-111157
    
    1/27/2004
    
    10.31+10.19+
    
    Stock Purchase Agreement,
dated as of March 21,
2003, by and among the
Registrant and the
stockholders identified on
the signature pages
    
    
    
    S-1/Amendment 3
File No. 333-111157
    
    7/6/2004
    
    10.27+10.20
    
    Amended and Restated Stock
Purchase Agreement, dated
July 27, 2004, by and
among the Registrant and
the
stockholders identified on
the signature pages
thereto
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.20
 22




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##### Table of Contents



Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number10.21
    
    Par Value Stock Purchase
Agreement, dated July 27,
2004, by and between the
Registrant and Novartis
Pharma AG
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.2110.22
    
    Concurrent Private
Placement Stock Purchase
Agreement, dated July 27,
2004, by and between the
Registrant and Novartis
Pharma AG
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.2210.23
    
    Final Settlement
Agreement, dated March 26,
2003, by and between the
Registrant and Sumitomo
Pharmaceuticals Co., Ltd.
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.1310.24
    
    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
File No. 333-111157
    
    5/28/2004
    
    10.3410.25#
    
    Amended and Restated 1998
Equity Incentive Plan
    
    
    
    S-1/Amendment 2
File No. 333-111157
    
    5/28/2004
    
    10.110.26#
    
    2004 Stock Incentive Plan
    
    
    
    S-1/Amendment 2
File No. 333-111157
    
    5/28/2004
    
    10.3210.27#
    
    Non-Employee Directors
Compensation Plan
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.2710.28#
    
    Form of Incentive Stock
Option Agreement for
awards granted pursuant to
the 2004 Stock Incentive
Plan
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.2810.29#
    
    Form of Nonqualifed Stock
Option Agreement for
awards granted pursuant to
the 2004 Stock Incentive
Plan
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    10.2910.30#
    
    Employment Agreement,
dated as of May 6, 2003,
by and between the
Registrant and Jean-Pierre
Sommadossi
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.510.31#
    
    Employment Agreement,
dated May 8, 2003, by and
between the Registrant and
Andrea Corcoran
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.6
 23




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##### Table of Contents



Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number10.32#
    
    Employment Agreement,
dated May 8, 2003, by and
between the Registrant and
James Egan
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.710.33#
    
    Employment Agreement,
dated May 8, 2003, by and
between the Registrant and
Nathaniel Brown
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.810.34#
    
    Employment Agreement,
dated July 28, 2003, by
and between the Registrant
and Guy Macdonald
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.1010.35#
    
    Employment Agreement,
dated December 1, 2003, by
and between
The Registrant and David
Arkowitz
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    10.1110.36#
    
    Employment Agreement dated
November 2, 2004 by and
between the Registrant and
David Shlaes
    
    
    
    10-Q
File No. 000-49839
    
    11/03/2004
    
    10.2010.37#
    
    Summary of 2005 Bonus Plan
    
    X21.1
    
    Subsidiaries of the Company
    
    
    
    S-1
File No. 333-111157
    
    12/15/2003
    
    21.123.1
    
    Consent of
PricewaterhouseCoopers LLP
Independent Registered
Public Accounting Firm
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    23.131.1
    
    Certification of Chief
Executive Officer pursuant
to Rule
13a-14(a)/15d-14(a) of the
Securities Exchange Act of
1934, as amended
(regarding Annual Report
on Form 10-K for the
fiscal year ended December
31, 2004)
    
    
    
    10-K 
File No. 000-49839
    
    3/17/2005
    
    31.131.2
    
    Certification of Chief
Financial Officer pursuant
to Rule
13a-14(a)/15d-14(a) of the
Securities Exchange Act of
1934, as amended
(regarding Annual Report
on Form 10-K for the
fiscal year ended December
31, 2004)
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    31.2
 24




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##### Table of Contents



Filed
    
    
    
    
    
    OriginalExhibit No.
    
    Description
    
    Herewith
    
    Form
    
    SEC Filing Date
    
    Exhibit Number31.3
    
    Certification of Chief
Executive Officer pursuant
to Rule
13a-14(a)/15d-14(a) of the
Securities Exchange Act of
1934, as amended
(regarding Amendment No. 1
on Form 10-K/A)
    
    X31.4
    
    Certification of Chief
Financial Officer pursuant
to Rule
13a-14(a)/15d-14(a) of the
Securities Exchange Act of
1934, as amended
(regarding Amendment No. 1
on Form 10-K/A)
    
    X32.1
    
    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
    
    
    
    10-K 
File No. 000-49839
    
    3/17/2005
    
    32.132.2
    
    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
    
    
    
    10-K
File No. 000-49839
    
    3/17/2005
    
    32.2
   #
    
    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 25