Exhibit 31.3
CERTIFICATIONS
I, Sudhir Agrawal, certify that:
1. I have reviewed this Amendment No. 1 to the Annual Report on Form 10-K 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 |
| Chairman, President and Chief Executive Officer |
Date: April 30, 2013
