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