**Exhibit 31.1**

**CERTIFICATION**

I, Argeris N. Karabelas, Ph.D., certify that:

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

#### 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;

#### 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;

#### 4.                                       The registrant’sother certifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) and internal control over financialreporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f))for the registrant and have:

##### a)                                      Designed suchdisclosure 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 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

##### d)                                     Disclosed in thisreport any change in the registrant’s internal control over financial reportingthat occurred during the registrant’s most recent fiscal quarter that hasmaterially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting; and

#### 5.                                       The registrant’sother certifying officer and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’sauditors and the audit committee of the registrant’s board of directors (orpersons performing the equivalent functions):

##### 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

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

| Dated: August 3, 2006 |   |                                          |
|----------------------------|--------|-----------------------------------------------|
|                       |   |                                          |
|                       |   | /s/ ARGERIS N. KARABELAS, Ph.D.               |
|                       |   | Argeris N. Karabelas, Ph.D.                   |
|                       |   | President and interim Chief Executive Officer |

 

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