**Exhibit31.1**

**CERTIFICATION**

I, Deborah Dunsire,certify that:

1.     I have reviewed this quarterly report on Form 10-Q of MillenniumPharmaceuticals, 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 Act Rules 13a-15(e)and 15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)          Designedsuch disclosure 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 such internalcontrol over financial reporting, or caused such internal control over financialreporting to be designed under our supervision, to provide reasonable assuranceregarding the reliability of financial reporting and the preparation offinancial statements for external purposes in accordance with generallyaccepted accounting principles;

(c)          Evaluatedthe effectiveness 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)         Disclosedin this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter (theregistrant’s fourth fiscal quarter in the case of an annual report) 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 recent evaluationof internal control over financial reporting, to the registrant’s auditors andthe audit committee of the registrant’s board of directors (or personsperforming the equivalent functions):

(a)          Allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial 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: October 31, 2006 |   | /s/ DEBORAH DUNSIRE                    |
|------------------------|--------|----------------------------------------|
|                   |   | Deborah Dunsire                        |
|                   |   | President and  Chief Executive Officer |

 

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