**Exhibit 31.1**

 

**CERTIFICATIONPURSUANT TO SECTION 302**

 

I, Jay D. Kranzler, certify that:

 

**1.****                                     **Ihave reviewed this Form 10-K of Cypress Bioscience, Inc.;

 

**2.****                                     **Basedon 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.****                                     **Basedon my knowledge, the financial statements, and other financial informationincluded in this report, fairly present in all material respects the financialcondition, results of operations and cash flows of the registrant as of, andfor, the periods presented in this report;

 

**4.****                                     **Theregistrant’s other certifying officers and I are responsible for establishingand maintaining disclosure 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)****                                 **designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

 

**(b)**                                  designed suchinternal control 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 effectiveness of the registrant’sdisclosure controls and procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, as of theend of the period covered by this report based on such evaluation; and

 

**(d)****                                 **disclosedin this report any change in the registrant’s internal controls over financialreporting that occurred during the registrant’s most recent fiscal quarter thathas materially affected, or is reasonably likely to materially affect, theregistrant’s internal controls over financial reporting; and

 

**5.****                                     **Theregistrant’s other certifying officers and I have disclosed, based on our mostrecent evaluation of internal controls over financial reporting, to the registrant’sauditors and the audit committee of registrant’s board of directors (or personsperforming the equivalent functions):

 

**(a)****                                 **allsignificant deficiencies and material weaknesses in the design or operation ofinternal controls over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial information; and

 

**(b)****                                 **anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal controls over financialreporting.

 
| Date: March 15, 2006 |
|---------------------------|
|                      |
| By:                       | /s/  JAY D. KRANZLER |   |
| Jay  D. Kranzler          |
| Chief Executive Officer   |

 

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