Exhibit 31.1**Certification of Chief Executive Officer Pursuant to Rule 13a-****14(a)****of the Securities ExchangeAct of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002**I, Peter J. Ungaro, certify that:     1. Ihave reviewed this Amendment No. 1 to the Annual Report on Form 10-K/A of Cray Inc.;     2. Based on my knowledge, this report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading with respect to the periodcovered by this report;     3. Based on my knowledge, the financial statements, and other financial information includedin this report, fairly present in all material respects the financial condition, results ofoperations 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 andmaintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules13a-15(f) and 15d-15(f)) for the registrant and we have: (a) designed such disclosure controls and procedures, or caused such disclosurecontrols and procedures to be designed under our supervision, to ensure thatmaterial information 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 internal control over financial reporting, or caused suchinternal control over financial reporting to be designed under our supervision, toprovide reasonable assurance regarding the reliability of financial reporting andthe preparation of financial statements for external purposes in accordance withgenerally accepted accounting principles;  (c) evaluated the effectiveness of the registrant’s disclosure controls andprocedures, and presented in this report our conclusions about the effectiveness ofthe disclosure controls and procedures as of the end of the period covered by thereport based on such evaluation; and  (d) disclosed in this report any change in the registrant’s internal control overfinancial reporting that occurred during the registrant’s most recent fiscalquarter 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 recentevaluation of internal control over financial reporting, to the registrant’s auditors and the auditcommittee 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 ofinternal control over financial reporting which are reasonably likely to adversely affectthe registrant’s ability to record, process, summarize and report financial information;and     (b) any fraud, whether or not material, that involves management or other employeeswho have a significant role in the registrant’s internal control over financial reporting.Date:June 19, 2007                             /s/ PETER J. UNGARO        Peter J. Ungaro        Chief Executive Officer and President