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     As filed with the Securities and Exchange Commission on July 27, 2001

                                                      Registration No. 333-57954

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549



                               Amendment No. 2 to

                        Form S-3 Registration Statement
                        Under the Securities Act of 1933


                                    CRAY INC.
             (Exact name of registrant as specified in its charter)



WASHINGTON                                                       93-0962605
                                                          
(State or other jurisdiction                                   (IRS Employer
of incorporation or organization)                            Identification No.)


                             411 First Avenue South
                                    Suite 600
                                Seattle, WA 98104
                           (206) 701-2000 (telephone)
                           (206) 701-2500 (facsimile)
       (Address, including zip code, and telephone and facsimile numbers,
              including area code, of principal executive offices)


                   Kenneth W. Johnson, Chief Financial Officer
                                    Cray Inc.
                             411 First Avenue South
                                    Suite 600
                                Seattle, WA 98104
                           (206) 701-2000 (telephone)
                           (206) 701-2500 (facsimile)
                            (Name, address, including
                 zip code, and telephone and facsimile numbers,
                   including area code, of agent for service)

                                    Copy to:
                               Christopher J. Voss
                                 Stoel Rives LLP
                          One Union Square, 36th Floor
                             Seattle, WA 98101-3197
                           (206) 624-0900 (telephone)
                           (206) 386-7500 (facsimile)

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
      From time to time after this registration statement becomes effective

If the only securities being registered on this Form are to be offered pursuant
to dividend or interest reinvestment plans, please check the following box. [ ]

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If any of the securities being registered on this Form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with a dividend or
interest reinvestment plan, check the following box. [X]

If this Form is filed to register additional securities for an offering pursuant
to Rule 462(b) under the Securities Act, please check the following box and list
the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ]

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under
the Securities Act, check the following box and list the Securities Act
registration number of the earlier effective registration statement for the same
offering. [ ]

If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]


The Registrant hereby amends this registration statement on such date or dates
as may be necessary to delay its effective date until the Registrant shall file
a further amendment which specifically states that this registration statement
shall thereafter become effective in accordance with section 8(a) of the
Securities Act of 1933 or until the registration statement shall become
effective on such date as the Securities and Exchange Commission, acting
pursuant to said section 8(a), may determine.

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PROSPECTUS, Subject to Completion, dated July 27, 2001


                                    CRAY INC.


                         500,000 shares of common stock


      These shares of common stock are being offered and sold by the selling
shareholder listed on page 3.

      The selling shareholder may sell the shares at fixed prices, market
prices, prices computed with formulas based on market prices, or at negotiated
prices, and may engage a broker or dealer to sell the shares. We will not
receive any proceeds from the sale of the shares, but will bear the costs
relating to the registration of the shares. Cray has also filed a registration
statement on Form S-3, registration no. 333-57972, for the resale of 5,139,408
shares of common stock issuable upon exercise of a common stock purchase
warrant owned by another shareholder. The resale of the shares issuable upon
exercise of the common stock purchase warrant may take place concurrently with
the shares offered for resale in this prospectus.

      Our common stock is traded on the Nasdaq National Market under the symbol
CRAY. On July 26, 2001, the closing price for our common stock was $2.62 per
share.

                         -------------------------------

      THE SHARES OFFERED IN THIS PROSPECTUS INVOLVE A HIGH DEGREE OF RISK. YOU
SHOULD CAREFULLY CONSIDER THE "FACTORS THAT COULD AFFECT FUTURE RESULTS"
CONTAINED IN OUR ANNUAL REPORT ON FORM 10-K FOR THE YEAR ENDING DECEMBER 31,
2000 AND IN OUR FUTURE FILINGS MADE WITH THE SECURITIES AND EXCHANGE COMMISSION,
WHICH ARE INCORPORATED BY REFERENCE IN THIS PROSPECTUS, IN DETERMINING WHETHER
TO PURCHASE SHARES OF OUR COMMON STOCK.


                        -------------------------------

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED THE SHARES, OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

                         -------------------------------


                 The date of this prospectus is _____ __, 2001.


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                                TABLE OF CONTENTS



      Section                                                          Page
      -------                                                          ----
                                                                    
      Our Business                                                       3

      Selling Shareholder                                                3

      Plan of Distribution                                               4

      Experts                                                            5

      Limitation of Liability and Indemnification                        5

      Information Incorporated by Reference                              6

      Available Information                                              7



      You should rely only on information contained or incorporated by reference
in this prospectus. See "Information Incorporated by Reference" on page 6.
Neither Cray nor the selling shareholder has authorized any other person to
provide you with information different from that contained in this prospectus.


      The shares of common stock are not being offered in any jurisdiction where
the offering is not permitted.


                                      -2-
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                                  OUR BUSINESS


      Cray Inc. designs, builds, sells and services high-performance computer
systems, sometimes referred to as supercomputers. Our executive offices are
located at Merrill Place, Suite 600, 411 First Avenue South, Seattle, WA
98104-2860, and our telephone number is (206) 701-2000.



                               SELLING SHAREHOLDER

      On April 2, 2000, we issued 1,000,000 shares of our common stock to
Silicon Graphics, Inc., the selling shareholder, in connection with our
acquisition of substantially all of the assets of Cray Research, a business unit
of Silicon Graphics. Our acquisition of Cray Research is described more fully in
our current report on Form 8-K for the event of April 2, 2000, as filed with the
Securities and Exchange Commission on April 17, 2000, and amendment no. 1
thereto on Form 8-K/A as filed with the Securities and Exchange Commission on
June 16, 2000.

      As of July 18, Silicon Graphics informed us that it had sold 500,000
shares pursuant to Rule 144 and that it held 500,000 shares of our common stock,
or approximately 1.2% of our issued and outstanding shares on such date. All of
the shares covered by this prospectus are being sold for the account of Silicon
Graphics. If all shares covered by this prospectus are sold, Silicon Graphics
will not hold any shares of our common stock. The shares covered by this
prospectus include only the shares of common stock issued to Silicon Graphics in
our acquisition of the Cray Research.





                                                          Ownership After Offering
                                                           if All Shares Offered
                            Shares Owned                    in Offering Are Sold
                            Before         Shares Being   ------------------------
      Selling Shareholder   Offering         Offered      Shares           Percent
      -------------------   ------------   ------------   ------           -------
                                                               
Silicon Graphics, Inc.       500,000          500,000       0                 0




      Silicon Graphics has not had any material relationship with us or any of
our affiliates within the past three years.

      Because Silicon Graphics may wish to be legally permitted to sell its
shares at any time it considers appropriate, we have agreed with Silicon
Graphics to file with the Securities and Exchange Commission, under the
Securities Act of 1933, a registration statement on Form S-3, of which this
prospectus forms a part, for the resale of the shares, and have agreed to
prepare and file amendments and supplements to the registration statement as may
be necessary to keep the registration statement effective until the shares are
no longer required to be registered for sale by Silicon Graphics.


                                      -3-
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                              PLAN OF DISTRIBUTION


      Cray is registering the shares covered by this prospectus for Silicon
Graphics. Silicon Graphics or its pledgees, donees, transferees or other
successors in interest may sell the shares in the over-the-counter market or by
other means, at market prices prevailing at the time of sale, at prices related
to prevailing market prices, or at negotiated prices. The shares may also be
sold by one or more of the following methods:


      -     a block trade in which a broker or dealer so engaged will attempt to
            sell the shares as agent but may position and resell a portion of
            the block, as principal, in order to facilitate the transaction;


      -     purchases by a broker or dealer, as principal, in a market maker
            capacity or by other means and resale by the broker or dealer for
            its account under the terms of the prospectus; or


      -     ordinary brokerage transactions and transactions in which a broker
            solicits purchases.


      Cray will pay the costs and fees of registering the shares, but Silicon
Graphics will pay any brokerage commissions, discounts or other expenses
relating to the sale of the shares. Cray and Silicon Graphics each have agreed
to indemnify the other against specified liabilities, including liabilities
arising under the Securities Act of 1933, that relate to statements or omissions
in the registration statement of which this prospectus forms a part.

      Regulation M under the Securities Exchange Act of 1934 provides that
during the period that any person is engaged in the distribution of our common
stock, the person engaged in the distribution generally may not purchase shares
of our common stock. Silicon Graphics is subject to applicable rules,
regulations and provisions of the Securities Act of 1933 and the Securities
Exchange Act of 1934, including, Regulation M, which may limit the timing of
purchases and sales of shares of our common stock by Silicon Graphics and may
affect the marketability of our common stock.

      Silicon Graphics may negotiate and pay brokers or dealers commissions,
discounts or concessions for their services. In making sales, brokers or dealers
engaged by Silicon Graphics may allow other brokers or dealers to participate.
However, Silicon Graphics and any brokers or dealers involved in the sale or
resale of the shares may qualify as underwriters within the meaning of the
section 2(a)(11) of the Securities Act of 1933. The brokers' or dealers'
commissions, discounts or concessions may qualify as underwriters' compensation
under the Securities Act of 1933. If Silicon Graphics qualifies as an
underwriter,it will be subject to the prospectus delivery requirements of
section 5(b)(2) of the Securities Act of 1933.


      Silicon Graphics may also:

      -     agree to indemnify any broker or dealer or agent against certain
            liabilities related to the selling of the shares, including
            liabilities arising under the Securities Act of 1933;


                                      -4-
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      -     transfer its shares in other ways not involving market makers or
            established trading markets, including directly by gift,
            distribution, or other transfer; or


      -     sell its shares under Rule 144 of the Securities Act of 1933 rather
            than under this prospectus, if the transaction meets the
            requirements of Rule 144.

           Upon notification by Silicon Graphics that any material arrangement
has been entered into with a broker or dealer for the sale of the shares through
a block trade, special offering, exchange distribution or secondary distribution
or a purchase by a broker or dealer, we will file a supplement to this
prospectus, if required, by Rule 424(b) under the Securities Act of 1933,
disclosing the material terms of the transaction.


                                  LEGAL MATTERS


      For purposes of this offering, Kenneth W. Johnson, Cray's general counsel,
is giving an opinion on the validity of the common shares. As of the date of
this prospectus, Mr. Johnson held 40,538 shares of Cray's common stock and
options exercisable for 270,000 shares of Cray's common stock.


                                     EXPERTS


        The financial statements incorporated in this prospectus by reference
from the Company's annual report on Form 10-K for the year ended December 31,
2000, have been audited by Deloitte & Touche LLP, independent auditors, as
stated in their report with respect thereto. The statements of assets acquired
and liabilities assumed of the Cray Research business unit of Silicon Graphics,
Inc. as of March 31, 2000, and the related statements of revenue and direct
operating expenses for the years ended June 30, 1998 and 1999 and the nine month
period ended March 31, 2000, included in the Form 8-K/A of Cray Inc., filed on
June 16, 2000 and incorporated by reference into this prospectus, have been
audited by Deloitte & Touche LLP, independent auditors, as stated in their
report with respect thereto (which report expresses an unqualified opinion and
includes an explanatory paragraph describing the expense allocations by Silicon
Graphics, Inc). These financial statements have been incorporated herein by
reference in reliance upon the reports of such firm given upon their authority
as experts in accounting and auditing.


                   LIMITATION OF LIABILITY AND INDEMNIFICATION


      Our restated articles of incorporation provide that, to the fullest extent
permitted by the Washington Business Corporation Act, our directors will not be
liable for monetary damages to Cray or its shareholders, excluding liability for
acts or omissions involving intentional misconduct or knowing violations of law,
illegal distributions or transactions from which the director receives benefits
to which the director is not legally entitled. Our restated bylaws provide that
Cray will indemnify its directors and, by action of the board of directors, may
indemnify its officers, employees and other


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agents to the fullest extent permitted by applicable law, except for any legal
proceeding that is initiated by our directors, officers, employees or agents
without authorization of the board of directors.

      We have been advised that, in the opinion of the Securities and Exchange
Commission, indemnification for liabilities arising under the Securities Act of
1933 for directors, officers and controlling persons is against public policy as
expressed in the Securities Act of 1933 and is not enforceable.


                      INFORMATION INCORPORATED BY REFERENCE


      The Securities and Exchange Commission allows us to incorporate by
reference our publicly-filed reports into this prospectus, which means that
information included in those reports is considered part of this prospectus.
Information that we file with the Securities and Exchange Commission after the
date of this prospectus will automatically update and supersede the information
contained in this prospectus. We incorporate by reference the following
documents filed with the Securities and Exchange Commission and any future
filings made with the Securities and Exchange Commission under sections 13(a),
13(c), 14 or 15(d) of the Securities Exchange Act of 1934:

      1.    Our annual report on Form 10-K for the year ended December 31, 2000;

      2.    Our quarterly report on Form 10-Q for the quarter ended March 31,
            2001;

      3.    Our definitive proxy statement, as filed with the Securities and
            Exchange Commission on April 9, 2001;

      4.    Our current report on Form 8-K for the event of May 10, 2001, as
            filed on May 14, 2001;

      5.    Our current report on Form 8-K for the event of April 3, 2001, as
            filed on April 13, 2001;

      6.    Our current report on Form 8-K for the event of February 7, 2001, as
            filed on February 15, 2001;

      7.    Our current report on Form 8-K for the event of December 15, 2000,
            as filed on January 4, 2001 and amended on July 27, 2001;

      8.    Our current report on Form 8-K for the event of April 3, 2000, as
            filed on April 5, 2000 and amended on June 16, 2000; and



                                      -6-
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       9.   The description of our common stock as described in our registration
            statement on Form SB-2 (registration no. 33-95460-LA), including any
            amendment or report filed for the purpose of updating the
            description, as incorporated by reference in our registration
            statement on Form 8-A (registration no. 0-26820), including the
            amendment on Form 8-A/A.

      We will furnish without charge to you, on written or oral request, a copy,
excluding exhibits, of any or all of the documents incorporated by reference.
You should direct any requests for documents to Investor Relations, Cray Inc.,
411 First Avenue South, Suite 600, Seattle, Washington 98104, telephone (206)
701-2000.


      The information relating to Cray contained in this prospectus is not
comprehensive and should be read together with the information contained in the
incorporated documents.


                              AVAILABLE INFORMATION


      This prospectus is part of a registration statement on Form S-3 that we
filed with the Securities and Exchange Commission. Information in the
registration statement has been omitted from this prospectus as permitted by the
Securities and Exchange Commission's rules.

      We file annual, quarterly and special reports and other information with
the Securities and Exchange Commission. You may read and copy the registration
statement and any other document that we file at the Securities and Exchange
Commission's public reference rooms located at Room 1024, Judiciary Plaza, 450
Fifth Street N.W., Washington, D.C. 20549; 7 World Trade Center, Suite 1300, New
York, New York 10048; and Citicorp Center, 500 West Madison Street, Suite 1400,
Chicago, Illinois 60661. Please call the Securities and Exchange Commission at
1-800-SEC-0330 for further information on the public reference rooms. Our
filings with the Securities and Exchange Commission are also available to you
free of charge at the Securities and Exchange Commission's web site at
http://www.sec.gov.

      Statements contained in this prospectus about the contents of any contract
or other document referred to describe only those portions of the contract or
document which are material. You should refer to the copy of the contract or
other document filed as an exhibit to the registration statement.


                                      -7-
   10

                                     PART II

                   INFORMATION NOT REQUIRED IN THE PROSPECTUS

Item 14. Other Expenses of Issuance and Distribution.

      All expenses in connection with the issuance and distribution of the
securities being registered will be paid by the Company. The following is an
itemized statement of these expenses (all amounts are estimated except for the
SEC fees):


                                                                
      SEC Registration fee ...........................             $   450

      Legal fees .....................................             $ 8,000

      Accountant's Fees ..............................             $ 3,000

      Miscellaneous ..................................             $   300
                                                                   -------

      Total ..........................................             $12,750
                                                                   =======



Item 15. Indemnification of Officers and Directors.

      Article XII of the Company's Restated Articles of Incorporation and
Section 11 of the Company's Restated Bylaws require indemnification of
directors, officers, employees and agents of the Company to the fullest extent
permitted by the Washington Business Corporation Act (the "Act"). Sections
23B.08.500 through 23B.08.600 of the Act authorize a court to award, or a
corporation's board of directors to grant, indemnification to directors and
officers on terms sufficiently broad to permit indemnification under certain
circumstances for liabilities arising under the Securities Act.

      Section 23B.08.320 of the Act authorizes a corporation to limit a
director's liability to the corporation or its shareholders for monetary damages
for acts or omissions as a director, except in certain circumstances involving
intentional misconduct, self-dealing or illegal corporate loans or
distributions, or any transaction from which the director personally receives a
benefit in money, property or services to which the director is not legally
entitled. Article XI of the Company's Restated Articles of Incorporation
contains provisions implementing, to the fullest extent permitted by Washington
law, such limitations on a director's liability to the Company and its
shareholders.


Item 16. Exhibits.


     5   Opinion on Legality


    23   Consent of Deloitte & Touche LLP

                                      II-1
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    24   Power of Attorney(1)


--------------
(1) Incorporated by reference to the Company's Registration Statement on Form
    S-3, Registration No. 333-57954, filed with the Commission on March 30,
    2001.

Item 17. Undertakings.

      (a)   The undersigned registrant hereby undertakes:

            (1)   To file, during any period in which offers or sales are being
                  made, a post-effective amendment to this Registration
                  Statement

                  (i)   To include any prospectus required by Section 10(a)(3)
                        of the Securities Act of 1933;

                  (ii)  To reflect in the prospectus any facts or events arising
                        after the effective date of this Registration Statement
                        (or the most recent post-effective amendment thereof)
                        that, individually or in the aggregate, represent a
                        fundamental change in the information set forth in this
                        Registration Statement; and

                  (iii) To include any material information with respect to the
                        plan of distribution not previously disclosed in the
                        registration statement or any material change to such
                        information in the registration statement;

                  provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do
                  not apply if the information required to be included in a
                  post-effective amendment by those paragraphs is contained in
                  periodic reports filed with or furnished to the Commission by
                  the registrant pursuant to Section 13 or Section 15(d) of the
                  Exchange Act that are incorporated by reference in the
                  registration statement;

            (2)   That, for the purpose of determining any liability under the
                  Securities Act, each post-effective amendment shall be deemed
                  to be a new registration statement relating to the securities
                  offered therein, and the offering of such securities at that
                  time shall be deemed to be the initial bona fide offering
                  thereof; and

            (3)   To remove from registration by means of a post-effective
                  amendment any of the securities being registered that remain
                  unsold at the termination of the offering.

      (b)   The undersigned registrant hereby undertakes that, for purposes of
            determining any liability under the Securities Act of 1933, each
            filing of the registrant's annual report pursuant to Section 13(a)
            or Section 15(d) of the Securities Exchange Act of 1934 that is
            incorporated by reference in the registration statement shall be
            deemed to be a new registration statement relating to the securities
            offered therein, and the offering of such securities at that time
            shall be deemed to be the initial bona fide offering thereof.

                                      II-2
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      (c)   Insofar as indemnification for liabilities arising under the
            Securities Act may be permitted to directors, officers and
            controlling persons of the registrant pursuant to the foregoing
            provisions, or otherwise, the registrant has been advised that in
            the opinion of the Commission such indemnification is against public
            policy as expressed in the Securities Act and is, therefore,
            unenforceable. In the event that a claim for indemnification against
            such liabilities (other than the payment by the registrant of
            expenses incurred or paid by a director, officer or controlling
            person of the registrant in the successful defense of any action,
            suit or proceeding) is asserted by such director, officer or
            controlling person in connection with the securities being
            registered, the registrant will, unless in the opinion of its
            counsel the matter has been settled by controlling precedent, submit
            to a court of appropriate jurisdiction the question, whether such
            indemnification by it is against public policy as expressed in the
            Securities Act and will be governed by the final adjudication of
            such issue.

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                                   SIGNATURES


      Pursuant to the requirements of the Securities Act of 1933, as amended,
the registrant certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form S-3 and has duly caused this
amendment no. 2 to registration statement No. 333-57954 to be signed on its
behalf by the undersigned, thereunto duly authorized, in the City of Seattle,
State of Washington, on July 27, 2001.


                                        CRAY INC.


                                        By: /s/ JAMES E. ROTTSOLK
                                            ------------------------------------
                                            James E. Rottsolk
                                            Chief Executive Officer

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      Pursuant to the requirements of the Securities Act of 1933, as amended,
this amendment no. 2 to registration statement no. 333-57954 has been signed by
the following persons in the capacities indicated below on the 27th day of
July, 2001:


Signature and Title

/s/ JAMES E. ROTTSOLK                                *
--------------------------------------  ----------------------------------------
James E. Rottsolk, Chairman of the      Daniel J. Evans, Director
Board of Directors and Chief Executive
Officer

               *                                     *
--------------------------------------  ----------------------------------------
Burton J. Smith, Director               Stephen C. Kiely, Director


               *                                     *
--------------------------------------  ----------------------------------------
Terren S. Peizer, Director              Kenneth W. Kennedy, Director


               *                                     *
--------------------------------------  ----------------------------------------
David N. Cutler, Director               William A. Owens, Director


               *                        /s/ KENNETH W. JOHNSON
--------------------------------------  ----------------------------------------
Dean D. Thornton, Director              Kenneth W. Johnson
                                        Chief Financial Officer

/s/ DOUGLAS C. RALPHS
--------------------------------------
Douglas C. Ralphs, Chief Accounting
Officer

/s/ JAMES E. ROTTSOLK
--------------------------------------
*James E. Rottsolk
Attorney-in-Fact