Exhibit 31.1
 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
  1.
    
    I have reviewed this Annual Report on Form 10-K of Idera Pharmaceuticals, Inc.;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;3.
    
    Based on my knowledge, the financial statements, and other financial information included in
this report, fairly present in all material respects the financial condition, results of operations
and cash flows of the registrant as of, and for, the periods presented in this report;4.
    
    The registrants other certifying officer and I are responsible for establishing and maintaining
disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and
internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and
15(d)-15(f)) for the registrant and have:
 a)
    
    Designed such disclosure controls and procedures, or caused such disclosure controls and
procedures to be designed under our supervision, to ensure that material information relating to
the registrant, including its consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this annual report is being prepared;b)
    
    Designed such internal control over financial reporting, or caused such internal control
over financial reporting to be designed under our supervision, to provide reasonable assurance
regarding the reliability of financial reporting and the preparation of financial statements for
external purposes in accordance with generally accepted accounting principles;c)
    
    Evaluated the effectiveness of the registrants disclosure controls and procedures and
presented in this annual report our conclusions about the effectiveness of the disclosure controls
and procedures, as of the end of the period covered by this report based on such evaluation; andd)
    
    Disclosed in this report any changes in the registrants internal control over financial
reporting that occurred during the registrants fourth fiscal quarter that has materially affected,
or is reasonably likely to materially affect, the registrants internal control over financial
reporting; and
 5.
    
    The registrants other certifying officer and I have disclosed, based on our most recent
evaluation of internal control over financial reporting, to the registrants auditors and the audit
committee of registrants board of directors (or persons performing the equivalent functions):
 a)
    
    All significant deficiencies and material weaknesses in the design or operation of internal
control over financial reporting which are reasonably likely to adversely affect the registrants
ability to record, process, summarize and report financial information; andb)
    
    Any fraud, whether or not material, that involves management or other employees who have a
significant role in the registrants internal control and financial reporting.
 /s/ Sudhir AgrawalSudhir AgrawalChief Executive Officer