**Exhibit 31.1**

 

**CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER**

 

I,Michael N. Chang, certify that:

 

1.I have reviewed this quarterly report on Form 10-Q of OptimerPharmaceuticals, Inc.;

 

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

 

3.Based on my knowledge, the financial statements, and other financialinformation included in this report, fairly present in all material respectsthe financial condition, results of operations and cash flows of the registrantas of, and for, the periods presented in this report;

 

4.The registrant’s other certifying officer and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) and internal control overfinancial reporting (as defined in Exchange Act Rules 13a-15(f) and15d-15(f)) for the registrant and have:

 

a)     designed such disclosurecontrols and procedures, or caused such disclosure controls and procedures tobe designed under our supervision, to ensure that material information relatingto the registrant, including its consolidated subsidiaries, is made known to usby others within those entities, particularly during the period in which thisreport is being prepared;

 

b)     designed such internalcontrol over financial reporting, or caused such internal control overfinancial reporting to be designed under our supervision, to provide reasonableassurance regarding the reliability of financial reporting and the preparationof financial statements for external purposes in accordance with generallyaccepted accounting principles;

 

c)     evaluated the effectivenessof the registrant’s disclosure controls and procedures and presented in thisreport our conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this report based on suchevaluation; and

 

d)     disclosed in this reportany change in the registrant’s internal control over financial reporting thatoccurred during the registrant’s most recent fiscal quarter (the registrant’sfourth fiscal quarter in the case of an annual report) that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and

 

5.The registrant’s other certifying officer and I have disclosed, based on ourmost recent evaluation of internal control over financial reporting, to theregistrant’s auditors and the audit committee of the registrant’s board ofdirectors (or persons performing the equivalent functions):

 

a)     all significant deficienciesand material weaknesses in the design or operation of internal control overfinancial reporting which are reasonably likely to adversely affect theregistrant’s ability to record, process, summarize and report financialinformation; and

 

b)     any fraud, whether or notmaterial, that involves management or other employees who have a significantrole in the registrant’s internal control over financial reporting.

 

Date:November 3, 2009

 
| /s/  Michael N. Chang                  |   |
|----------------------------------------|--------|
| Michael  N. Chang                      |   |
| President  and Chief Executive Officer |   |

 

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