**Exhibit 31.2**

 

**CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER**

 

I,John D. Prunty, certify that:

 

1.I have reviewed this quarterly report on Form 10-Q of Optimer Pharmaceuticals,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)) for the registrant 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)        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

 

c)         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 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 deficiencies andmaterial 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 not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 

 

Date:November 9, 2007 

 
| /s/ John D. Prunty                                                                        |   |
|-------------------------------------------------------------------------------------------|--------|
| John  D. Prunty                                                                           |   |
| Vice-President  and Chief Financial Officer  (Principal Financial and Accounting Officer) |   |

 

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