**EXHIBIT 31.1**

 

**CERTIFICATIONOF CHIEF EXECUTIVE OFFICER**

** **

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

 

| 1.     | I have reviewed  this Quarterly Report on Form 10-Q of CombiMatrix Corporation;                                                                                                                                                                                                                                                                                    |
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| 2.     | Based on my  knowledge, this report does not contain any untrue statement of a material  fact or omit to state a material fact necessary to make the statements made,  in light of the circumstances under which such statements were made, not  misleading with respect to the period covered by this report;                                                          |
|   |                                                                                                                                                                                                                                                                                                                                                                    |
| 3.     | Based on my  knowledge, the financial statements, and other financial information included  in this report, fairly present in all material respects the financial  condition, results of operations and cash flows of the registrant as of, and  for, the periods presented in this report;                                                                             |
|   |                                                                                                                                                                                                                                                                                                                                                                    |
| 4.     | The registrant’s  other certifying officer and I are responsible for establishing and  maintaining disclosure controls and procedures (as defined in Exchange Act  Rules 13a-15(e) and 15d-15(e)) and internal controls over financial  reporting (as defined in the Exchange Act Rules 13a-15(f) and  15d-15(f)) for the registrant and have: |
|   |                                                                                                                                                                                                                                                                                                                                                                    |   |
|   | a.                                                                                                                                                                                                                                                                                                                                                                      | Designed such  disclosure controls and procedures, or caused such disclosure controls and  procedures to be designed under our supervision, to ensure that material information  relating to the registrant, including its consolidated subsidiaries, is made  known to us by others within those entities, particularly during the period  in which this report is being prepared; |
|   |                                                                                                                                                                                                                                                                                                                                                                    |   |
|   | b.                                                                                                                                                                                                                                                                                                                                                                      | Designed such  internal control over financial reporting, or caused such internal control  over financial reporting to be designed under our supervision, to provide  reasonable assurance regarding the reliability of financial reporting and the  preparation of financial statements for external purposes in accordance with  generally accepted accounting principles; |
|   |                                                                                                                                                                                                                                                                                                                                                                    |   |
|   | c.                                                                                                                                                                                                                                                                                                                                                                      | Evaluated the  effectiveness of the registrant’s disclosure controls and procedures and  presented in this report our conclusions about the effectiveness of the  disclosure controls and procedures, as of the end of the period covered by  this report based on such evaluation; and |
|   |                                                                                                                                                                                                                                                                                                                                                                    |   |
|   | d.                                                                                                                                                                                                                                                                                                                                                                      | Disclosed in  this report any change in the registrant’s internal control over financial  reporting that occurred during the registrant’s most recent fiscal quarter  that has materially affected, or is reasonably likely to materially affect,  the registrant’s internal control over financial reporting; and |
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| 5.     | The registrant’s  other certifying officer and I have disclosed, based on our most recent  evaluation of internal control over financial reporting, to the registrant’s  auditors and the audit committee of the registrant’s board of directors:                                                                                                        |
|   |                                                                                                                                                                                                                                                                                                                                                                    |   |
|   | a.                                                                                                                                                                                                                                                                                                                                                                      | All significant  deficiencies and material weaknesses in the design or operation of internal  control over financial reporting which are 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 involves management or other employees who have a significant  role in the registrant’s internal control over financial reporting. |
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| Date:    August 14, 2009 | /s/ AMIT KUMAR, PH.D.                                                       |
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|                                    | Amit Kumar, Ph.D.

Chief Executive Officer

*(Principal Executive Officer)* |

 

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