Exhibit 31.3

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

I, Sudhir Agrawal, certify that:

     1. I have reviewed this Amendment No. 1 on Form 10-K/A of Idera Pharmaceuticals, Inc.; and

     2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report.

/s/ Sudhir Agrawal Sudhir Agrawal

Chief Executive Officer

Dated: December 24, 2008

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