**Exhibit 31.1**

**CERTIFICATION**

I, Michael W.Bonney, certify that:

1.                 I have reviewedthis annual report on Form 10-K of Cubist Pharmaceuticals, Inc.;

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

3.                 Based on myknowledge, the financial statements, and other financial information includedin this annual 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 annual report;

4.                 The registrant’sother certifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for theregistrant and have:

(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 thisannual report is being prepared;

(b)         designed such internalcontrol 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 annual report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisannual report based on such evaluation; and

(d)         disclosed in this annualreport any change in the registrant’s internal control over financial reportingthat occurred during the registrant’s most recent fiscal quarter (the registrant’sfourth fiscal quarter in the case of an annual report) that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal 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)         anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.
| Date: March 1, 2007               |   |
|----------------------------------------|--------|
| /s/ MICHAEL W. BONNEY                  |   |
| Michael W. Bonney                      |   |
| President and  Chief Executive Officer |   |

 

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