##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-K/A
 (Amendment No. 1)
  þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the Fiscal Year Ended December 31, 2008
 OR
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 Commission File Number: 001-31918
 IDERA PHARMACEUTICALS, INC.
 (Exact name of Registrant as specified in its certificate of incorporation)
 Delaware
    
    04-3072298(State or other jurisdiction
    
    (I.R.S. Employerof incorporation or organization)
    
    Identification No.)167 Sidney StreetCambridge, Massachusetts
    
    02139(Address of principal executive offices)
    
    (Zip Code)
 (617) 679-5500
(Registrants telephone number, including area code)
 Securities registered pursuant to Section 12(b) of the Act:
 Title of Class:
    
    Name of Each Exchange on Which Registered:Common Stock, $.001 par value
    
    NASDAQ Global Market(Including Associated Preferred Stock Purchase Rights)
 Securities registered pursuant to Section 12(g) of the Act: None
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  Large accelerated filer oAccelerated filer þNon-accelerated filer o(Do not check if a smaller reporting company)Smaller reporting company o o þ
  DOCUMENTS INCORPORATED BY REFERENCE




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TABLE OF CONTENTS  Exhibit IndexSIGNATUREEX-10.55 Amendment dated February 12, 2009 to the License AgreementEX-31.3 Section 302 Certification of CEOEX-31.4 Section 302 Certification of CFO    Table of Contents  EXPLANATORY NOTE




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##### Table of Contents



Exhibit Index
 Incorporated by ReferenceFiled with this
    
    Form or
    
    
    
    SEC FileExhibit Number
    
    Description
    
    Form 10-K/A
    
    Schedule
    
    Filing Date with SEC
    
    Number3.1
    
    Restated Certificate of Incorporation of Idera
Pharmaceuticals, Inc., as amended.
    
    
    
    10-Q
    
    August 1, 2008
    
    001-319183.2
    
    Amended and Restated Bylaws of Idera Pharmaceuticals,
Inc.
    
    
    
    S-1
    
    November 6, 1995
    
    33-990243.3
    
    Certificate of Ownership and Merger.
    
    
    
    8-K
    
    September 15, 2005
    
    001-319184.1
    
    Specimen Certificate for shares of Common Stock, $.001
par value, of Idera Pharmaceuticals, Inc.
    
    
    
    S-1
    
    December 8, 1995
    
    33-990244.2
    
    Rights Agreement dated December 10, 2001 by and between
Idera Pharmaceuticals, Inc. and Mellon Investor
Services LLC, as rights agent.
    
    
    
    S-2
    
    October 10, 2003
    
    333-1096304.3
    
    Amendment No. 1 to Rights Agreement dated as of August
27, 2003 between the Company and Mellon Investor
Services LLC, as rights agent.
    
    
    
    8-K
    
    August 29, 2003
    
    000-273524.4
    
    Amendment No. 2 to Rights Agreement dated as of March
24, 2006 between the Company and Mellon Investor
Services LLC, as rights agent.
    
    
    
    8-K
    
    March 29, 2006
    
    001-319184.5
    
    Amendment No. 3 to Rights Agreement dated January 16,
2007 between the Company and Mellon Investor Services,
LLC, as rights agent.
    
    
    
    8-K
    
    January 17, 2007
    
    001-3191810.1
    
    2008 Stock Incentive Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.2
    
    2005 Stock Incentive Plan, as amended
    
    
    
    10-Q
    
    August 14, 2006
    
    001-3191810.3
    
    1995 Stock Option Plan.
    
    
    
    S-1
    
    November 6, 1995
    
    33-9902410.4
    
    1995 Director Stock Option Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.5
    
    1995 Employee Stock Purchase Plan, as amended.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.6
    
    Employment Agreement dated October 19, 2005 between
Idera Pharmaceuticals, Inc. and Dr. Sudhir Agrawal.
    
    
    
    10-Q
    
    November 9, 2005
    
    001-3191810.7
    
    Amendment, dated December 17, 2008 to Employment
Agreement by and between the Idera Pharmaceuticals,
Inc. and Dr. Sudhir Agrawal dated October 19, 2005.
    
    
    
    8-K
    
    December 18, 2008
    
    001-3191810.8
    
    Employment Offer Letter dated November 8, 2007 by and
between Idera Pharmaceuticals, Inc. and Louis J.
Arcudi, III.
    
    
    
    10-K/A
    
    December 24, 2008
    
    001-3191810.9
    
    Amendment dated December 17, 2008 to Employment Offer
Letter by and between Idera Pharmaceuticals, Inc. and
Louis J. Arcudi, III, Dated November 8, 2007.
    
    
    
    8-K
    
    December 18, 2008
    
    001-3191810.10
    
    Non-Employee Director Compensation Program Effective
January 1, 2008.
    
    
    
    10-K
    
    March 11, 2008
    
    001-3191810.11
    
    Amended and Restated 1997 Stock Incentive Plan.
    
    
    
    10-Q
    
    May 15, 2001
    
    000-2735210.12
    
    Non-Employee Director Nonstatutory Stock Option
Agreement Granted under 1997 Stock Incentive Plan.
    
    
    
    10-K
    
    March 25, 2005
    
    001-31918




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##### Table of Contents



Incorporated by ReferenceFiled with this
    
    Form or
    
    
    
    SEC FileExhibit Number
    
    Description
    
    Form 10-K/A
    
    Schedule
    
    Filing Date with SEC
    
    Number10.13
    
    Form of Incentive Stock Option Agreement Granted Under
the 2005 Stock Incentive Plan.
    
    
    
    8-K
    
    June 21, 2005
    
    001-3191810.14
    
    Form of Nonstatutory Stock Option Agreement Granted
Under the 2005 Stock Incentive Plan.
    
    
    
    8-K
    
    June 21, 2005
    
    001-3191810.15
    
    Form of Restricted Stock Agreement Under the 2005 Stock
Incentive Plan.
    
    
    
    10-Q
    
    August 1, 2007
    
    001-3191810.16
    
    Form of Incentive Stock Option Agreement Granted Under
the 2008 Stock Incentive Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.17
    
    Form of Nonstatutory Stock Option Agreement Granted
Under the 2008 Stock Incentive Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.18
    
    Form of Nonstatutory Stock Option Agreement
(Non-Employee Directors) Granted Under the 2008 Stock
Incentive Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.19
    
    Form of Restricted Stock Agreement Under the 2008 Stock
Incentive Plan.
    
    
    
    8-K
    
    June 10, 2008
    
    001-3191810.20
    
    Executive Stock Option Agreement for 1,260,000 Options
effective as of July 25, 2001 between Idera
Pharmaceuticals, Inc. and Dr. Sudhir Agrawal.
    
    
    
    10-Q
    
    October 24, 2002
    
    000-2735210.21
    
    Executive Stock Option Agreement for 550,000 Options
effective as of July 25, 2001 between Idera
Pharmaceuticals, Inc. and Dr. Sudhir Agrawal.
    
    
    
    10-Q
    
    October 24, 2002
    
    000-2735210.22
    
    Executive Stock Option Agreement for 500,000 Options
effective as of July 25, 2001 between Idera
Pharmaceuticals, Inc. and Dr. Sudhir Agrawal.
    
    
    
    10-Q
    
    October 24, 2002
    
    000-2735210.23
    
    License Agreement dated February 21, 1990 and restated
as of September 8, 1993 between Idera Pharmaceuticals,
Inc. and University of Massachusetts Medical Center.
    
    
    
    S-1
    
    November 6, 1995
    
    33-9902410.24
    
    Amendment No. 1 to License Agreement, dated as of
February 21, 1990 and restated as of September 8, 1993,
by and between University of Massachusetts Medical
Center and Idera Pharmaceuticals, Inc., dated as of
November 26, 1996.
    
    
    
    10-Q
    
    August 14, 1997
    
    000-2735210.25
    
    Collaboration and License Agreement by and between Isis
Pharmaceuticals, Inc., and Idera Pharmaceuticals, Inc.,
dated May 24, 2001.
    
    
    
    10-Q
    
    August 20, 2001
    
    000-2735210.26
    
    Amendment No. 1 to the Collaboration and License
Agreement, dated as of May 24, 2001 by and between Isis
Pharmaceuticals, Inc. and Idera Pharmaceuticals, Inc.,
dated as of August 14, 2002.
    
    
    
    10-K
    
    March 31, 2003
    
    000-2735210.27
    
    Master Agreement relating to the Cross License of
Certain Intellectual Property and Collaboration by and
between Isis Pharmaceuticals, Inc. and Idera
Pharmaceuticals, Inc., dated May 24, 2001.
    
    
    
    10-Q
    
    August 20, 2001
    
    000-2735210.28
    
    Unit Purchase Agreement by and among Idera
Pharmaceuticals, Inc. and certain persons and entities
listed therein, dated April 1, 1998.
    
    
    
    10-K
    
    April 1, 2002
    
    000-27352




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##### Table of Contents



Incorporated by ReferenceFiled with this
    
    Form or
    
    
    
    SEC FileExhibit Number
    
    Description
    
    Form 10-K/A
    
    Schedule
    
    Filing Date with SEC
    
    Number10.29
    
    Registration Rights Agreement, dated as of August 28,
2003 by and among Idera Pharmaceuticals, Inc., the
Purchasers and the Agents.
    
    
    
    S-2
    
    October 10, 2003
    
    333-10963010.30
    
    Form of Common Stock Purchase Warrant issued to
purchasers of units in a private placement on August
28, 2003 and August 29, 2003.
    
    
    
    S-2
    
    October 10, 2003
    
    333-10963010.31
    
    Form of Common Stock Purchase Warrant issued to
selected dealers and placement agents on August 28,
2003 in connection with a private placement.
    
    
    
    S-2
    
    October 10, 2003
    
    333-10963010.32
    
    Registration Rights Agreement, dated August 27, 2004 by
and among Idera Pharmaceuticals, Inc., Pillar
Investment Limited and Purchasers.
    
    
    
    10-Q
    
    November 12, 2004
    
    001-3191810.33
    
    Form of Warrants issued to investors and the placement
agent in connection with Idera Pharmaceuticals, Inc.
August 27, 2004 financing.
    
    
    
    10-Q
    
    November 12, 2004
    
    001-3191810.34
    
    Research Collaboration and Option Agreement by and
between Idera Pharmaceuticals, Inc. and Novartis
International Pharmaceutical Ltd.
    
    
    
    10-Q
    
    August 9, 2005
    
    001-3191810.35
    
    License, Development and Commercialization Agreement by
and between Idera Pharmaceuticals, Inc and Novartis
International Pharmaceutical Ltd.
    
    
    
    10-Q
    
    August 9, 2005
    
    001-3191810.36
    
    Engagement letter, dated May 20, 2005, by and among
Idera Pharmaceuticals, Inc. and Pillar Investment
Limited.
    
    
    
    10-Q
    
    August 9, 2005
    
    001-3191810.37
    
    Consulting Agreement dated as of January 1, 2008
between Idera Pharmaceuticals, Inc. and Karr Pharma
Consulting, LLC.
    
    
    
    10-K
    
    March 11, 2008
    
    001-3191810.38
    
    Amendment dated December 16, 2008 to Consulting
Agreement dated as of January 1, 2008 between Idera
Pharmaceuticals, Inc. and Karr Pharma Consulting, LLC.
    
    
    
    10-K
    
    March 11, 2009
    
    001-3191810.39
    
    Registration Rights Agreement dated as of May 20, 2005
by and among Idera Pharmaceuticals, Inc., Purchasers
and Pillar Investment Limited.
    
    
    
    10-Q
    
    August 9, 2005
    
    001-3191810.40
    
    Common Stock Purchase Warrant issued to Pillar
Investment Limited in connection with the May 20, 2005
Financing.
    
    
    
    10-Q
    
    August 9, 2005
    
    001-3191810.41
    
    Common Stock Purchase Agreement, dated March 24, 2006,
by and among the Company and the Investors named
therein.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.42
    
    Registration Rights Agreement, dated March 24, 2006, by
and among the Company and the Investors named therein.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.43
    
    Amendment No. 1 to the Common Stock Purchase Agreement,
dated March 24, 2006, by and among the Company and the
Investors named therein.
    
    
    
    10-Q
    
    August 14, 2006
    
    001-3191810.44
    
    Form of Warrant issued to Investors in the Companys
March 24, 2006 Private Financing.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.45
    
    Common Stock Purchase Agreement, dated
March 24, 2006,
by and between the Company and Biotech Shares Ltd.
    
    
    
    8-K
    
    March 29, 2006
    
    001-31918




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##### Table of Contents



Incorporated by ReferenceFiled with this
    
    Form or
    
    
    
    SEC FileExhibit Number
    
    Description
    
    Form 10-K/A
    
    Schedule
    
    Filing Date with SEC
    
    Number10.46
    
    Amendment No. 1 to the Common Stock Purchase Agreement,
dated
March 24, 2006, by and among the Company and
Biotech Shares Ltd.
    
    
    
    10-Q
    
    November 13, 2006
    
    001-3191810.47
    
    Engagement Letter, dated March 24, 2006, between the
Company and Youssef El Zein.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.48
    
    Registration Rights Agreement, dated March 24, 2006, by
and among the Company, Biotech Shares Ltd. and Youssef
El Zein.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.49
    
    Warrant issued to Biotech Shares Ltd. on March 24, 2006.
    
    
    
    8-K
    
    March 29, 2006
    
    001-3191810.50
    
    Exclusive License and Research Collaboration Agreement
by and between Merck & Co., Inc. and Idera
Pharmaceuticals, Inc., dated December 8, 2006.
    
    
    
    8-K
    
    March 6, 2007
    
    001-3191810.51
    
    Amendment No. 1 to the Registration Rights Agreement
dated March 24, 2006, by and among the Company and
Biotech Shares Ltd.
    
    
    
    10-Q
    
    August 14, 2006
    
    001-3191810.52
    
    Promissory Note dated June 12, 2007 made by Idera
Pharmaceuticals, Inc. in favor of General Electric
Capital Corporation.
    
    
    
    10-Q
    
    August 1, 2007
    
    001-3191810.53
    
    Master Security Agreement dated June 12, 2007 by and
between Idera Pharmaceuticals, Inc. and General
Electric Capital Corporation.
    
    
    
    10-Q
    
    August 1, 2007
    
    001-3191810.54
    
    License Agreement by and between Merck KGaA and Idera
Pharmaceuticals, Inc., dated December 18, 2007.
    
    
    
    10-K
    
    March 11, 2008
    
    001-3191810.55
    
    Amendment dated February 12, 2009 to the License
Agreement by and between Merck KGaA and Idera
Pharmaceuticals, Inc., dated December 18, 2007.
    
    X23.1
    
    Consent of Independent Registered Public Accounting
Firm.
    
    
    
    10-K
    
    March 11, 2009
    
    001-3191831.1
    
    Certification of Chief Executive Officer pursuant to
Exchange Act Rules 13a-14 and 15d-14, as adopted
pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
    
    
    
    10-K
    
    March 11, 2009
    
    001-3191831.2
    
    Certification of Chief Financial Officer pursuant to
Exchange Act Rules 13a-14 and 15d-14, as adopted
pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
    
    
    
    10-K
    
    March 11, 2009
    
    001-3191831.3
    
    Certification of Chief Executive Officer pursuant to
Exchange Act Rules 13a-14 and 15d-14, as adopted
pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
    
    X31.4
    
    Certification of Chief Financial Officer pursuant to
Exchange Act Rules 13a-14 and 15d-14, as adopted
pursuant to Section 302 of Sarbanes-Oxley Act of 2002.
    
    X32.1
    
    Certification of Chief Executive Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906
of the Sarbanes-Oxley Act of 2002.
    
    
    
    10-K
    
    March 11, 2009
    
    001-31918




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##### Table of Contents



Incorporated by ReferenceFiled with this
    
    Form or
    
    
    
    SEC FileExhibit Number
    
    Description
    
    Form 10-K/A
    
    Schedule
    
    Filing Date with SEC
    
    Number32.2
    
    Certification of Chief Financial Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906
of the Sarbanes-Oxley Act of 2002.
    
    
    
    10-K
    
    March 11, 2009
    
    001-31918
 
 
    
    Confidential treatment granted as to certain portions, which portions are omitted and filed separately with the Commission.
    
    Management contract or compensatory plan or arrangement required to be filed as an Exhibit to the Annual Report on Form
10-K.




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##### Table of Contents



SIGNATURE
 th
 IDERA PHARMACEUTICALS, INC.By:
    /s/  Sudhir AgrawalSudhir AgrawalPresident, Chief Executive Officer
and Chief Scientific Officer