**Exhibit 31.1**

 

**CERTIFICATIONOF PRINCIPAL EXECUTIVE OFFICERPURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002**

 

I, Michael N. Chang, certify that:

 

1. I have reviewed this annual report on Form 10-Kof Optimer Pharmaceuticals, Inc.;

 

2. Based on my knowledge, this report does not containany untrue statement of a material fact or omit to state a material factnecessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this report;

 

3. Based on my knowledge, the financial statements,and other financial information included in this report, fairly present in allmaterial respects the financial condition, results of operations and cash flowsof the registrant as of, and for, the periods presented in this report;

 

4. The registrant’s other certifying officer and I areresponsible for establishing and maintaining disclosure controls and procedures(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for theregistrant and have:

 

a)                          designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including any consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisreport is being prepared;

 

b)                         designed such internal control overfinancial reporting, or caused such internal control over financial reportingto be designed under our supervision, to provide reasonable assurance regardingthe reliability of financial reporting and the preparation of financialstatements for external purposes in accordance with generally acceptedaccounting principles;

 

c)                          evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this reportour 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 report any change inthe registrant’s internal control over financial reporting that occurred duringthe registrant’s most recent fiscal quarter (the registrant’s fourth fiscalquarter in the case of an annual report) that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial reporting; and

 

5. The registrant’s other certifying officer and Ihave disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofthe registrant’s board of directors (or persons performing the equivalentfunctions):

 

a)              all significant deficiencies and material weaknessesin the design or operation of internal control over financial reporting whichare reasonably likely to adversely affect the registrant’s ability to record,process, summarize and report financial information; and

 

b)             any fraud, whether or not material, that involvesmanagement or other employees who have a significant role in the registrant’sinternal control over financial reporting.

 

Date: March 12, 2009

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

 

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