**Exhibit 31.1**

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**CERTIFICATION**

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I, Kenneth M.Bate, certify that:

 

#### 1.                                       I have reviewedthis Quarterly Report on Form 10-Q of NitroMed, Inc.;

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#### 2.                                       Based on myknowledge, this report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, inlight of the circumstances under which such statements were made, notmisleading with respect to the period covered by this report;

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#### 3.                                       Based on myknowledge, the financial statements, and other financial information includedin 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;

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#### 4.                                       I amresponsible for establishing and maintaining disclosure controls and procedures(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) andinternal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and15d-15(f)) for the registrant and have:

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##### a)                                      Designed such disclosurecontrols and procedures, or caused such disclosure controls and procedures tobe designed under our supervision, to ensure that material information relatingto the registrant, including its consolidated subsidiaries, is made known to usby others within those entities, particularly during the period in which thisreport is being prepared;

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##### 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;

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##### c)                                      Evaluated theeffectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

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##### d)                                     Disclosed inthis report any change in the registrant’s internal control 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 control over financial reporting; and

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#### 5.                                       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 (or persons performing the equivalentfunctions):

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##### a)                                      All significantdeficiencies and material weaknesses in the design or operation of internalcontrol over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

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##### b)                                     Any fraud,whether or not material, that involves management or other employees who have asignificant role in the registrant’s internal control over financial reporting.

 
| Dated:  November 6, 2008 |                                                                                                                                     |
|-------------------------------|------------------------------------------------------------------------------------------------------------------------------------------|
|                          | /s/  KENNETH M. BATE                                                                                                                     |
|                          | Kenneth  M. Bate                                                                                                                         |
|                          | President,  Chief Executive Officer and Interim Chief Financial  Officer*(Principal Executive Officer and Principal  Financial Officer)* |

 

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