##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549
   Form 10-K/A (Amendment No. 1)
 (Mark One)þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THESECURITIES EXCHANGE ACT OF 1934For the fiscal year ended December 31, 2004ORo
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THESECURITIES EXCHANGE ACT OF 1934
 For the transition period fromto Commission file number 0-31261 AtheroGenics, Inc.  Georgia
    
    58-2108232(State or other jurisdiction of
    
    (I.R.S. Employer Identification Number)incorporation or organization)8995 Westside Parkway,
    
    (678) 336-2500Alpharetta, Georgia 30004
    
    (Registrants telephone number, including area code)(Address of principal executive offices, including zip code)
 Securities registered pursuant to Section 12(b) of the Exchange Act: None Securities registered pursuant to Section 12(g) of the Exchange Act: Common Stock, No Par Value
Common Stock Purchase Rights   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 this Form 10-K. o Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule
12b-2 of the Act) Yes þ No o The aggregate market value of shares of voting stock held by nonaffiliates of the registrant,
computed by reference to the closing price of $19.03 as reported on the Nasdaq National Market as
of the last business day of AtheroGenics most recently completed second fiscal quarter (June 30,
2004), was approximately $422,239,543. AtheroGenics has no nonvoting common equity. The number of shares outstanding of the registrants common stock, as of March 8, 2005:
37,668,445. Documents Incorporated by Reference: Portions of the proxy statement filed pursuant to Regulation 14A under the Securities Exchange
Act of 1934 with respect to the 2005 Annual Meeting of Shareholders are incorporated herein by
reference in Part III.




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##### Table of Contents



EXPLANATORY NOTE AtheroGenics, Inc. is filing this Amendment No. 1 to its Annual Report on Form 10-K for the
fiscal year ended December 31, 2004 solely to make corrections
to the exhibit index and to add exhibits that were inadvertently omitted from the
list of exhibits in Item 15 of Part IV of the Form 10-K. The complete text of Item 15 is included
in this Amendment pursuant to Rule 12b-15 promulgated under the Securities and Exchange Act of
1934, as amended (the Exchange Act). In addition, Item 15 includes the certifications required
pursuant to Rules 13a-14(a)/15d-14(a) of the Exchange Act, which have been re-executed and re-filed
as of the date of this Amendment as Exhibits 31.3 and 31.4, respectively. With the exception of the foregoing corrections, no other information in the Annual Report on
Form 10-K for the fiscal year ended December 31, 2004 has been supplemented, updated or amended.




---



TABLE OF CONTENTS  EXPLANATORY NOTEPART IVItem 15. Exhibits and Financial Statement SchedulesSIGNATURESEXHIBIT INDEXEX-3.01 FOURTH AMENDED AND RESTATED ARTICLES OF INCORPORATIONEX-4.04 GLOBAL 4 1/2% CONVERTIBLE NOTE DUE 2008EX-31.3 SECTION 302 CERTIFICATION OF THE CEOEX-31.4 SECTION 302 CERTIFICATION OF THE CFO    Table of Contents  
 PART IV 
 Item 15.Exhibits and Financial Statement Schedules  (1)
    Financial Statements, filed as part of this reportReport of Independent Registered Public Accounting FirmBalance Sheets as of December 31, 2004 and 2003Statements of Operations for the years ended December 31, 2004, 2003 and 2002Statements Shareholders (Deficit) Equity for the years ended December 31, 2004,
2003 and 2002Statements of Cash Flows for the years ended December 31, 2004, 2003 and 2002Notes to Financial Statements(2)
    Financial Statement SchedulesNo financial statement schedules are provided, because the information called for
is not required or is shown either in the financial statements or the notes
thereto.(3)
    Listing of Exhibits Exhibit No.
    
    
    
    Description3.01*
    
    
    
    Fourth Amended and Restated Articles of Incorporation of AtheroGenics, Inc.3.02
    
    
    
    Third Amended and Restated Bylaws of AtheroGenics, Inc., as amended (filed as an exhibit
of the same number with AtheroGenics Annual Report on Form 10-K for the year ended
December 31, 2001 and incorporated herein by reference).4.01
    
    
    
    Form of Common Stock Certificate (filed as Exhibit 4.01 to Amendment No. 4 to
AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on August
4, 2000 and incorporated herein by reference).4.02
    
    
    
    Rights Agreement dated as of November 9, 2001 between AtheroGenics, Inc. and American
Stock Transfer & Trust Company, as Rights Agent (filed as Exhibit 4.4 of AtheroGenics
Form 8-K on November 19, 2001 and incorporated herein by reference).4.03
    
    
    
    Indenture dated August 19, 2003 between AtheroGenics, Inc. and The Bank of New York
Trust Company of Florida N.A., as Trustee (filed as Exhibit 4.1 to AtheroGenics
Registration Statement on Form S-3, Registration No. 333-110160, on October 31, 2003,
and incorporated herein by reference).4.04*
    
    
    

    Global 4 1/2% Convertible Note Due 2008.10.01
    
    
    
    Amended and Restated Master Rights Agreement dated October 31, 1995, as amended by First
Amendment dated November 1, 1995; Second Amendment dated July 30, 1996; Third Amendment
dated April 13, 1999; Fourth Amendment dated May 11, 1999; and Fifth Amendment dated
August 30, 1999 (filed as Exhibit 4.02 to AtheroGenics Registration Statement on Form
S-1, Registration No. 333-31140, on February 25, 2000 and incorporated herein by
reference).10.02+
    
    
    
    Exclusive License Agreement dated July 17, 1998 between The Regents of the University of
California and AtheroGenics, Inc. (filed as Exhibit 10.02 to Amendment No. 4 to
AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on August
4, 2000 and incorporated herein by reference).
 2




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##### Table of Contents



Exhibit No.
    
    
    
    Description10.03+
    
    
    
    License Agreement dated January 11, 1995 between Emory University and AtheroGenics, Inc.
(filed as Exhibit 10.03 to Amendment No. 2 to AtheroGenics Registration Statement on
Form S-1, Registration No. 333-31140, on July 13, 2000 and incorporated herein by
reference).10.04+
    
    
    
    Patent Purchase Agreement dated April 26, 1995 between AtheroGenics, Inc. and Sampath
Parthasarathy, together with Services Agreement dated April 26, 1995 between
AtheroGenics, Inc. and Sampath Parthasarathy (filed as Exhibit 10.04 to Amendment No. 2
to AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on July
13, 2000 and incorporated herein by reference).10.05+
    
    
    
    Sponsored Research Agreement dated October 14, 1996 between Emory University and
AtheroGenics, Inc. (filed as Exhibit 10.05 to Amendment No. 2 to AtheroGenics
Registration Statement on Form S-1, Registration No. 333-31140, on July 13, 2000 and
incorporated herein by reference).10.06#
    
    
    
    AtheroGenics, Inc. 1995 Stock Option Plan, together with form of nonqualified stock
option agreement (filed as Exhibit 10.07 to AtheroGenics Registration Statement on Form
S-1, Registration No. 333-31140, on February 25, 2000 and incorporated herein by
reference).10.07#
    
    
    
    AtheroGenics, Inc. 1997 Equity Ownership Plan, as amended by Amendment No. 1 and
Amendment No. 2 (filed as Exhibit 10.08 to Amendment No. 2 to AtheroGenics Registration
Statement on Form S-1, Registration No. 333-31140, on July 13, 2000 and incorporated
herein by reference).10.08
    
    
    
    Preferred Shares Purchase Warrant dated August 24, 1998 between AtheroGenics, Inc. and
certain Lenders named therein (filed as Exhibit 10.09 to AtheroGenics Registration
Statement on Form S-1, Registration No. 333-31140, on February 25, 2000 and incorporated
herein by reference).10.09
    
    
    
    Series C Convertible Preferred Stock Purchase Warrants of AtheroGenics, Inc. (filed as
Exhibit 10.10 to AtheroGenics Registration Statement on Form S-1, Registration No.
333-31140, on February 25, 2000 and incorporated herein by reference).10.10
    
    
    
    Promissory Note dated April 1, 1999 between Inhibitex, Inc. and AtheroGenics, Inc.
(filed as Exhibit 10.11 to AtheroGenics Registration Statement on Form S-1,
Registration No. 333-31140, on February 25, 2000 and incorporated herein by reference).10.11++
    
    
    
    Lease Agreement dated June 19, 1998 between Cousins Properties, Inc. and AtheroGenics,
Inc. (filed as Exhibit 10.12 to AtheroGenics Registration Statement on Form S-1,
Registration No. 333-31140, on February 25, 2000 and incorporated herein by reference).10.12#
    
    
    
    Employment Agreement dated March 1, 2001 between AtheroGenics, Inc. and Russell M.
Medford (filed as Exhibit 10.14 to AtheroGenics Annual Report on Form 10-K for the year
ended December 31, 2000, and incorporated herein by reference).10.13
    
    
    
    Amendment dated January 1, 2001 to Promissory Note dated April 1, 1999 between
Inhibitex, Inc. and AtheroGenics, Inc. (filed as Exhibit 10.15 to AtheroGenics Annual
Report on Form 10-K for the year ended December 31, 2000, and incorporated herein by
reference).10.14+
    
    
    
    Exclusive License Agreement dated as of June 29, 2001 between AtheroGenics, Inc. and
National Jewish Medical and Research Center (filed as Exhibit 10.17 to Amendment No. 1
to AtheroGenics Registration Statement on Form S-1, Registration No. 333-64228, on July
23, 2001 and incorporated herein by reference).10.15#
    
    
    
    AtheroGenics, Inc. 2001 Equity Ownership Plan (filed as Appendix B to the proxy
statement on Schedule 14A for AtheroGenics 2001 Annual Shareholders Meeting as filed
on March 22, 2001 and incorporated herein by reference).10.16
    
    
    
    Equipment Term Note dated March 6, 2002 between AtheroGenics, Inc. and Silicon Valley
Bank (filed as Exhibit 10.20(b) to AtheroGenics Quarterly Report on Form 10-Q for the
quarter ended March 31, 2002 and incorporated herein by reference).10.17
    
    
    
    Loan and Security Agreement dated March 6, 2002 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.20(c) to AtheroGenics Quarterly Report on Form 10-Q
for the quarter ended March 31, 2002 and incorporated herein by reference).
 3




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##### Table of Contents



Exhibit No.
    
    
    
    Description10.18#
    
    
    
    Promissory Note and Stock Pledge Agreement dated as of April 15, 2002 between
AtheroGenics, Inc. and Mark P. Colonnese (filed as Exhibit 10.21 to AtheroGenics
Quarterly Report on Form 10-Q for the quarter ended June 30, 2002 and incorporated
herein by reference).10.19#
    
    
    
    Separation and Consulting Agreement and General Release dated as of October 3, 2002
between AtheroGenics, Inc. and Mitchell Glass, M.D. (filed as Exhibit 10.22 to
AtheroGenics Quarterly Report on Form 10-Q for the quarter ended September 30, 2002 and
incorporated herein by reference).10.20
    
    
    
    First Loan Modification dated June 20, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank.
(filed as Exhibit 10.23 to AtheroGenics Quarterly Report on Form 10-Q for the quarter
ended June 30, 2003 and incorporated herein by reference).10.21
    
    
    
    Purchase Agreement dated August 19, 2003 between AtheroGenics, Inc. and the Initial
Purchasers named therein (filed as Exhibit 10.24 to AtheroGenics Quarterly Report on
Form 10-Q for the quarter ended September 30, 2003 and incorporated herein by
reference).10.22
    
    
    
    Registration Rights Agreement dated as of August 19, 2003 among AtheroGenics, Inc., as
Issuer, and Morgan Stanley & Co., Incorporated, Lehman Brothers, Inc., and Adams,
Harkness & Hill, Inc., as Initial Purchasers (filed as Exhibit 4.2 to AtheroGenics
Registration Statement on Form S-3, Registration No. 333-110160, on October 31, 2003,
and incorporated herein by reference).10.23
    
    
    
    Second Loan Modification dated August 13, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.25 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.24
    
    
    
    Third Loan Modification dated December 29, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.26 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.25
    
    
    
    Negative Pledge Agreement dated December 29, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.27 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.26#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Mark P.
Colonnese (filed as Exhibit 10.28 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.27#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Martin A.
Wasserman (filed as Exhibit 10.29 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.28#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Robert A. D.
Scott (filed as Exhibit 10.30 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.29#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and W. Charles
Montgomery (filed as Exhibit 10.31 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.30#
    
    
    
    AtheroGenics, Inc. 2004 Equity Ownership Plan (filed as Appendix B to the proxy
statement on Schedule 14A for AtheroGenics 2004 Annual Shareholders Meeting as filed
on March 26, 2004 and incorporated herein by reference).10.31#
    
    
    
    AtheroGenics, Inc. 2004 Equity Ownership Plan form of incentive equity ownership
agreement and form of directors nonqualified equity ownership agreement (filed as
Exhibit 10.33 to AtheroGenics Annual Report on Form 10-K for the year ended December
31, 2004 on March 16, 2005 and incorporated herein by reference).10.32#
    
    
    
    Summary of non-employee director
compensation (filed as the first paragraph under the caption Director
Compensation in the proxy statement on Schedule 14A for AtheroGenics 2005 Annual
Meeting of Shareholders as filed with the SEC on March 28, 2005 and incorporated herein
by reference).23.01**
    
    
    
    Consent of Ernst & Young LLP.24.01**
    
    
    
    Powers of Attorney.31.1**
    
    
    
    Certifications of Chief Executive Officer under Rule 13a-14(a).31.2**
    
    
    
    Certifications of Chief Financial Officer under Rule 13a-14(a).31.3*
    
    
    
    Certifications of Chief Executive
Officer under Rule 13c-14(a).31.4*
    
    
    
    Certifications of Chief Financial
Officer under Rule 13a-14(a).32**
    
    
    
    Certifications of Chief Executive Officer and Chief Financial Officer under Section 1350.
   *
    
    Filed herewith. 4




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##### Table of Contents



**
    
    Filed as the exhibit of the same number with AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2004 on March 16, 2005 and incorporated herein by reference.+
    
    Certain confidential information contained in this document has been
omitted and filed separately with the Commission pursuant to a request
for confidential treatment under Rule 406 of the Securities Act of
1933, as amended.++
    
    We agree to furnish supplementally to the Commission a copy of any
omitted schedule or exhibit to this agreement upon request by the
Commission.#
    
    Management contract or compensatory plan or arrangement. 5




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SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934,
the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto
duly authorized, on April 5, 2005. ATHEROGENICS, INC.By:
    /s/RUSSELL M. MEDFORDRussell M. Medford, M.D., Ph.D.President and Chief Executive Officer Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been
signed below by the following persons on behalf of the registrant and in the capacities and on the
dates indicated. Name
    
    Title
    
    DatePrincipal Executive Officer:/s/RUSSELL M. MEDFORD
    
    President and Chief Executive
    
    April 5, 2005Russell M. Medford
    
    Officer, DirectorPrincipal Financial and PrincipalAccounting Officer:/s/MARK P. COLONNESE
    
    Senior Vice President of Finance
    
    April 5, 2005Mark P. Colonnese
    
    and Administration and ChiefFinancial OfficerAdditional Directors:*
    
    Director
    
    April 5, 2005Michael A. Henos*
    
    Director
    
    April 5, 2005R. Wayne Alexander*
    
    Director
    
    April 5, 2005David Bearman*
    
    Director
    
    April 5, 2005Vaughn D. Bryson*
    
    Director
    
    April 5, 2005T. Forcht Dagi*
    
    Director
    
    April 5, 2005Arthur M. Pappas*
    
    Director
    
    April 5, 2005William A. Scott*
    
    Director
    
    April 5, 2005Stephen G. Sudovar
 *By:
    /s/MARK P. COLONNESEMark P. ColonneseAttorney-in-fact
 6




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##### Table of Contents



EXHIBIT INDEX Exhibit No.
    
    
    
    Description3.01*
    
    
    
    Fourth Amended and Restated Articles of Incorporation of AtheroGenics, Inc.3.02
    
    
    
    Third Amended and Restated Bylaws of AtheroGenics, Inc., as amended (filed as an exhibit
of the same number with AtheroGenics Annual Report on Form 10-K for the year ended
December 31, 2001 and incorporated herein by reference).4.01
    
    
    
    Form of Common Stock Certificate (filed as Exhibit 4.01 to Amendment No. 4 to
AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on August
4, 2000 and incorporated herein by reference).4.02
    
    
    
    Rights Agreement dated as of November 9, 2001 between AtheroGenics, Inc. and American
Stock Transfer & Trust Company, as Rights Agent (filed as Exhibit 4.4 of AtheroGenics
Form 8-K on November 19, 2001 and incorporated herein by reference).4.03
    
    
    
    Indenture dated August 19, 2003 between AtheroGenics, Inc. and The Bank of New York
Trust Company of Florida N.A., as Trustee (filed as Exhibit 4.1 to AtheroGenics
Registration Statement on Form S-3, Registration No. 333-110160, on October 31, 2003,
and incorporated herein by reference).4.04*
    
    
    
    Global 4 1/2% Convertible Note Due 2008.10.01
    
    
    
    Amended and Restated Master Rights Agreement dated October 31, 1995, as amended by First
Amendment dated November 1, 1995; Second Amendment dated July 30, 1996; Third Amendment
dated April 13, 1999; Fourth Amendment dated May 11, 1999; and Fifth Amendment dated
August 30, 1999 (filed as Exhibit 4.02 to AtheroGenics Registration Statement on Form
S-1, Registration No. 333-31140, on February 25, 2000 and incorporated herein by
reference).

10.02+
    
    
    
    Exclusive License Agreement dated July 17, 1998 between The Regents of the University of
California and AtheroGenics, Inc. (filed as Exhibit 10.02 to Amendment No. 4 to
AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on August
4, 2000 and incorporated herein by reference).10.03+
    
    
    
    License Agreement dated January 11, 1995 between Emory University and AtheroGenics, Inc.
(filed as Exhibit 10.03 to Amendment No. 2 to AtheroGenics Registration Statement on
Form S-1, Registration No. 333-31140, on July 13, 2000 and incorporated herein by
reference).10.04+
    
    
    
    Patent Purchase Agreement dated April 26, 1995 between AtheroGenics, Inc. and Sampath
Parthasarathy, together with Services Agreement dated April 26, 1995 between
AtheroGenics, Inc. and Sampath Parthasarathy (filed as Exhibit 10.04 to Amendment No. 2
to AtheroGenics Registration Statement on Form S-1, Registration No. 333-31140, on July
13, 2000 and incorporated herein by reference).10.05+
    
    
    
    Sponsored Research Agreement dated October 14, 1996 between Emory University and
AtheroGenics, Inc. (filed as Exhibit 10.05 to Amendment No. 2 to AtheroGenics
Registration Statement on Form S-1, Registration No. 333-31140, on July 13, 2000 and
incorporated herein by reference).10.06#
    
    
    
    AtheroGenics, Inc. 1995 Stock Option Plan, together with form of nonqualified stock
option agreement (filed as Exhibit 10.07 to AtheroGenics Registration Statement on Form
S-1, Registration No. 333-31140, on February 25, 2000 and incorporated herein by
reference).10.07#
    
    
    
    AtheroGenics, Inc. 1997 Equity Ownership Plan, as amended by Amendment No. 1 and
Amendment No. 2 (filed as Exhibit 10.08 to Amendment No. 2 to AtheroGenics Registration
Statement on Form S-1, Registration No. 333-31140, on July 13, 2000 and incorporated
herein by reference).10.08
    
    
    
    Preferred Shares Purchase Warrant dated August 24, 1998 between AtheroGenics, Inc. and
certain Lenders named therein (filed as Exhibit 10.09 to AtheroGenics Registration
Statement on Form S-1, Registration No. 333-31140, on February 25, 2000 and incorporated
herein by reference).10.09
    
    
    
    Series C Convertible Preferred Stock Purchase Warrants of AtheroGenics, Inc. (filed as
Exhibit 10.10 to AtheroGenics Registration Statement on Form S-1, Registration No.
333-31140, on February 25, 2000 and incorporated herein by reference).
 7




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##### Table of Contents



Exhibit No.
    
    
    
    Description10.10
    
    
    
    Promissory Note dated April 1, 1999 between Inhibitex, Inc. and AtheroGenics, Inc.
(filed as Exhibit 10.11 to AtheroGenics Registration Statement on Form S-1,
Registration No. 333-31140, on February 25, 2000 and incorporated herein by reference).10.11++
    
    
    
    Lease Agreement dated June 19, 1998 between Cousins Properties, Inc. and AtheroGenics,
Inc. (filed as Exhibit 10.12 to AtheroGenics Registration Statement on Form S-1,
Registration No. 333-31140, on February 25, 2000 and incorporated herein by reference).10.12#
    
    
    
    Employment Agreement dated March 1, 2001 between AtheroGenics, Inc. and Russell M.
Medford (filed as Exhibit 10.14 to AtheroGenics Annual Report on Form 10-K for the year
ended December 31, 2000, and incorporated herein by reference).10.13
    
    
    
    Amendment dated January 1, 2001 to Promissory Note dated April 1, 1999 between
Inhibitex, Inc. and AtheroGenics, Inc. (filed as Exhibit 10.15 to AtheroGenics Annual
Report on Form 10-K for the year ended December 31, 2000, and incorporated herein by
reference).10.14+
    
    
    
    Exclusive License Agreement dated as of June 29, 2001 between AtheroGenics, Inc. and
National Jewish Medical and Research Center (filed as Exhibit 10.17 to Amendment No. 1
to AtheroGenics Registration Statement on Form S-1, Registration No. 333-64228, on July
23, 2001 and incorporated herein by reference).10.15#
    
    
    
    AtheroGenics, Inc. 2001 Equity Ownership Plan (filed as Appendix B to the proxy
statement on Schedule 14A for AtheroGenics 2001 Annual Shareholders Meeting as filed
on March 22, 2001 and incorporated herein by reference).10.16
    
    
    
    Equipment Term Note dated March 6, 2002 between AtheroGenics, Inc. and Silicon Valley
Bank (filed as Exhibit 10.20(b) to AtheroGenics Quarterly Report on Form 10-Q for the
quarter ended March 31, 2002 and incorporated herein by reference).10.17
    
    
    
    Loan and Security Agreement dated March 6, 2002 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.20(c) to AtheroGenics Quarterly Report on Form 10-Q
for the quarter ended March 31, 2002 and incorporated herein by reference).10.18#
    
    
    
    Promissory Note and Stock Pledge Agreement dated as of April 15, 2002 between
AtheroGenics, Inc. and Mark P. Colonnese (filed as Exhibit 10.21 to AtheroGenics
Quarterly Report on Form 10-Q for the quarter ended June 30, 2002 and incorporated
herein by reference).10.19#
    
    
    
    Separation and Consulting Agreement and General Release dated as of October 3, 2002
between AtheroGenics, Inc. and Mitchell Glass, M.D. (filed as Exhibit 10.22 to
AtheroGenics Quarterly Report on Form 10-Q for the quarter ended September 30, 2002 and
incorporated herein by reference).10.20
    
    
    
    First Loan Modification dated June 20, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank.
(filed as Exhibit 10.23 to AtheroGenics Quarterly Report on Form 10-Q for the quarter
ended June 30, 2003 and incorporated herein by reference).10.21
    
    
    
    Purchase Agreement dated August 19, 2003 between AtheroGenics, Inc. and the Initial
Purchasers named therein (filed as Exhibit 10.24 to AtheroGenics Quarterly Report on
Form 10-Q for the quarter ended September 30, 2003 and incorporated herein by
reference).10.22
    
    
    
    Registration Rights Agreement dated as of August 19, 2003 among AtheroGenics, Inc., as
Issuer, and Morgan Stanley & Co., Incorporated, Lehman Brothers, Inc., and Adams,
Harkness & Hill, Inc., as Initial Purchasers (filed as Exhibit 4.2 to AtheroGenics
Registration Statement on Form S-3, Registration No. 333-110160, on October 31, 2003,
and incorporated herein by reference).10.23
    
    
    
    Second Loan Modification dated August 13, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.25 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.24
    
    
    
    Third Loan Modification dated December 29, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.26 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.25
    
    
    
    Negative Pledge Agreement dated December 29, 2003 between AtheroGenics, Inc. and Silicon
Valley Bank (filed as Exhibit 10.27 to AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2003 and incorporated herein by reference).10.26#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Mark P.
Colonnese (filed as Exhibit 10.28 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).
 8




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##### Table of Contents



Exhibit No.
    
    
    
    Description10.27#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Martin A.
Wasserman (filed as Exhibit 10.29 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.28#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and Robert A. D.
Scott (filed as Exhibit 10.30 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.29#
    
    
    
    Employment Agreement dated December 22, 2004 between AtheroGenics, Inc. and W. Charles
Montgomery (filed as Exhibit 10.31 to AtheroGenics Form 8-K on December 22, 2004 and
incorporated herein by reference).10.30#
    
    
    
    AtheroGenics, Inc. 2004 Equity Ownership Plan (filed as Appendix B to the proxy
statement on Schedule 14A for AtheroGenics 2004 Annual Shareholders Meeting as filed
on March 26, 2004 and incorporated herein by reference).10.31#
    
    
    
    AtheroGenics, Inc. 2004 Equity Ownership Plan form of incentive equity ownership
agreement and form of directors nonqualified equity ownership agreement (filed as
Exhibit 10.33 to AtheroGenics Annual Report on Form 10-K for the year ended December
31, 2004 on March 16, 2005 and incorporated herein by reference).10.32#
    
    
    
    Summary of non-employee director compensation (filed under the caption Director
Compensation in the proxy statement on Schedule 14A for AtheroGenics 2005 Annual
Meeting of Shareholders as filed with the SEC on March 28, 2005 and incorporated herein
by reference).23.01**
    
    
    

    Consent of Ernst & Young LLP.24.01**
    
    
    
    Powers of Attorney.31.1**
    
    
    
    Certifications of Chief Executive Officer under Rule 13a-14(a).31.2**
    
    
    
    Certifications of Chief Financial Officer under Rule 13a-14(a).31.3*
    
    
    
    Certifications of Chief Executive
Officer under Rule 13a-14(a).31.4*
    
    
    
    Certifications of Chief Financial
Officer under Rule 13a-14(a).32**
    
    
    
    Certifications of Chief Executive Officer and Chief Financial Officer under Section 1350.
   *
    
    Filed herewith.**
    
    Filed as the exhibit of the same number with AtheroGenics Annual Report on Form 10-K for the
year ended December 31, 2004 on March 16, 2005 and incorporated herein by reference.+
    
    Certain confidential information contained in this document has been
omitted and filed separately with the Commission pursuant to a request
for confidential treatment under Rule 406 of the Securities Act of
1933, as amended.++
    
    We agree to furnish supplementally to the Commission a copy of any
omitted schedule or exhibit to this agreement upon request by the
Commission.#
    
    Management contract or compensatory plan or
arrangement. 9