**EXHIBIT 31.1**

 

**CERTIFICATIONOF CHIEF EXECUTIVE OFFICER**

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I, Amit Kumar, Ph.D.,certify that:

 

1.     I have reviewed this Quarterly Report on Form 10-Qof CombiMatrix Corporation;

 

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, andother 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)) andinternal controls over financial reporting (as defined in the Exchange Act Rules 13a-15(f) and15d-15(f)) for the registrant and have:

 

a.     Designed such disclosure controls and procedures, orcaused such disclosure controls and procedures to be designed under oursupervision, to ensure that material information relating to the registrant,including its consolidated subsidiaries, is made known to us by others withinthose entities, particularly during the period in which this report is beingprepared;

 

b.    Designed such internal control over financialreporting, or caused such internal control over financial reporting to bedesigned under our supervision, to provide reasonable assurance regarding thereliability of financial reporting and the preparation of financial statementsfor external purposes in accordance with generally accepted accountingprinciples;

 

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.    Disclosed in this report any change in the registrant’sinternal control over financial reporting that occurred during the registrant’smost recent fiscal quarter that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control over financialreporting; and

 

5.     The registrant’s other certifying officer and I havedisclosed, 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:

 

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:   November 10,  2008 | /s/ AMIT KUMAR, PH.D.                                                       |
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|                                           | Amit Kumar, Ph.D.   Chief Executive Officer *(Principal Executive Officer)* |

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