**EXHIBIT 31.1**

 

**CERTIFICATION OF CHIEF EXECUTIVEOFFICER**

 

I,Amit Kumar, certify that:

 
| 1.     | I  have reviewed this Quarterly Report on Form 10-Q of CombiMatrix  Corporation;                                                                                                                                                                                                                          |
|--------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |                                                                                                                                                                                                                                                                                                           |
| 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)) 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  (the registrant’s fourth fiscal quarter in the case of an annual report) that  has materially affected, or is reasonably likely to materially affect, the  registrant’s internal control over financial reporting; and |

 
| 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 (or persons performing the equivalent functions): |
|----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

 
| 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.                                                                                                 |

 
| Date: May 15,  2008 | /s/ Amit Kumar                                                     |
|--------------------------|--------------------------------------------------------------------|
|                     | Amit Kumar  Chief Executive Officer*(Principal Executive Officer)* |

 

----