**Exhibit 31.1**

 

**CERTIFICATIONOF PRINCIPAL EXECUTIVE OFFICER**

 

I, Michael N. Chang,certify that:

 

1. I have reviewed thisquarterly report on Form 10-Q of Optimer Pharmaceuticals, Inc.;

 

2. Based on my knowledge,this report does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

 

3. Based on my knowledge,the financial statements, and other financial information included in thisreport, fairly present in all material respects the financial condition,results of operations and cash flows of the registrant as of, and for, theperiods presented in this report;

 

4. The registrant’s othercertifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant andhave:

 

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 its 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 in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarterin the case of an annual report) that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control over financialreporting; and

 

5. The registrant’s othercertifying officer and I have disclosed, based on our most recent evaluation ofinternal control over financial reporting, to the registrant’s auditors and theaudit committee of the registrant’s board of directors (or persons performingthe equivalent functions):

 

a)     all significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

 

b)    any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 

Date: May 8, 2009

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

 

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