1

     As filed with the Securities and Exchange Commission on April 19, 2001
                                                      Registration No. 333-57954


                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549



                               Amendment No. 1 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. [ ]

   2

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.

   3


PROSPECTUS, Subject to Completion, dated April 19, 2001


                                    CRAY INC.

                        1,000,000 shares of Common Stock


      These shares of Common Stock are being offered and sold from time to time
by one of our current shareholders.

      The selling shareholder may sell the shares from time to time 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. For
additional information on the selling shareholder's possible methods of sale,
you should refer to the section of this prospectus entitled "Plan of
Distribution" on page 4. We will not receive any proceeds from the sale of the
shares, but will bear the costs relating to the registration of the shares.


      Our Common Stock is traded on the Nasdaq National Market under the symbol
"CRAY." On April 12, 2001, the closing price for our Common Stock was $1.91 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.

   4

                                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-
   5

                                  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. ("SGI"), the selling shareholder, in connection with our
acquisition of substantially all of the assets of the Cray Research business
unit of SGI (the "Cray Acquisition"). The Cray Acquisition 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 (the "SEC") on April 17, 2000, and
Amendment No. 1 thereto on Form 8-K/A as filed with the SEC on June 16, 2000.

      As of March 23, 2001 SGI held 1,000,000 shares of our common stock, or
approximately 2.5% of our issued and outstanding shares on such date. All of the
shares covered by this prospectus are being sold for the account of SGI. If all
shares covered by this prospectus are sold, SGI will not hold any shares of our
common stock. The shares covered by this prospectus include only the shares of
common stock issued to SGI in the Cray Acquisition.



      Selling Shareholder   Shares Owned   Shares Being   Ownership After Offering
      -------------------   Prior to         Offered        if All Shares Offered
                            Offering       ------------        Hereby Are Sold
                                                          Shares           Percent
                                                          ------           -------
                                                               
Silicon Graphics, Inc.     1,000,000        1,000,000       0                 0


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

      In recognition of the fact that SGI may wish to be legally permitted to
sell its shares when it deems appropriate, we have agreed with SGI to file with
the SEC, under the Securities Act of 1933 (the "Securities Act"), a registration
statement on Form S-3, of which this prospectus forms a part, with respect to
the resale of the shares, and have agreed to prepare and file such 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 SGI.

                                      -3-
   6

                              PLAN OF DISTRIBUTION

      Cray is registering the shares covered by this prospectus for SGI. SGI or
its pledgees, donees, transferees or other successors in interest may sell the
shares in the over-the-counter market or otherwise, at market prices prevailing
at the time of sale, at prices related to prevailing market prices, or at
negotiated prices. In addition, the shares may 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 otherwise and resale by the broker or dealer for its
            account pursuant to their 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 SGI will
pay any brokerage commissions, discounts or other expenses relating to the sale
of the shares. Cray and SGI each have agreed to indemnify the other against
certain liabilities, including liabilities arising under the Securities Act,
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, as so defined
in Regulation M, of our common stock, such person generally may not purchase
shares of our common stock. SGI is subject to applicable provisions of the
Securities Act and the Securities Exchange Act of 1934 and the rules and
regulations thereunder, including, without limitation, Regulation M, which
provisions may limit the timing of purchases and sales of shares of our common
stock by SGI. The foregoing may affect the marketability of our common stock.

      SGI may negotiate and pay brokers or dealers commissions, discounts or
concessions for their services. In effecting sales, brokers or dealers engaged
by SGI may allow other broker or dealers to participate. However, SGI 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.
In addition, the brokers' or dealers' commissions, discounts or concessions may
qualify as underwriters' compensation under the Securities Act. If SGI qualifies
as an "underwriter," it will be subject to the prospectus delivery requirements
of Section 5(b)(2) of the Securities Act.


      In addition to selling its shares under this prospectus, SGI may:

      -     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;

                                      -4-
   7

      -     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 rather than
            under this prospectus, if the transaction meets the requirements of
            Rule 144.

           Upon notification by SGI 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, pursuant to Rule 424(b) under the Securities Act, disclosing the
material terms of the transaction.


                                  LEGAL MATTERS

      For purposes of this offering, Kenneth W. Johnson, the Company's General
Counsel, is giving an opinion on the validity of the common shares. As of the
date of this prospectus, Mr. Johnson held 39,713 shares of the Company's common
stock and options exercisable for 270,000 shares of the Company'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, which is incorporated herein by reference, and have
been so incorporated in reliance upon the report 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, however,
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

                                      -5-
   8
agents to the fullest extent permitted by applicable law, except for any legal
proceeding that is initiated by such directors, officers, employees or agents
without authorization of the Board of Directors.

      Insofar as indemnification for liabilities arising under the Securities
Act may be permitted to directors, officers and controlling persons of Cray
pursuant to the foregoing provisions, or otherwise, we have been advised that,
in the opinion of the SEC, such indemnification is against public policy as
expressed in the Securities Act and is, therefore, unenforceable.


                      INFORMATION INCORPORATED BY REFERENCE

      The SEC 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 SEC
subsequent to the date of this prospectus will automatically update and
supersede the information contained in this prospectus. We incorporate by
reference the documents listed below and any future filings made with the SEC
under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934
until the selling shareholders have sold all the shares.

      The following documents filed with the SEC are incorporated by reference
in this prospectus:


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

      2.    Our Definitive Proxy Statement, as filed with the SEC on April 9,
            2001;

      3.    Our Current Report on Form 8-K for the event of April 3, 2001, as
            filed on April 13, 2001; and



                                      -6-
   9


       4.   The description of our common stock set forth in our Registration
            Statement on Form SB-2 (Registration No. 33-95460-LA), including any
            amendment or report filed for the purpose of updating such
            description, as incorporated by reference in our Registration
            Statement on Form 8-A (Registration No. 0-26820), including the
            amendment thereto on Form 8-A/A.


      We will furnish without charge to you, on written or oral request, a copy
of any or all of the documents incorporated by reference, other than exhibits to
such documents. 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 SEC. Certain information in the Registration Statement has been
omitted from this prospectus in accordance with SEC rules.

      We file annual, quarterly and special reports and other information with
the SEC. You may read and copy the Registration Statement and any other document
that we file at the SEC'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 SEC at
1-800-SEC-0330 for further information on the public reference rooms. Our SEC
filings are also available to you free of charge at the SEC's web site at
http://www.sec.gov.

      Statements contained in this prospectus as to the contents of any contract
or other document referred to are not necessarily complete. You should refer to
the copy of such 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(1)


    23   Consent of Deloitte & Touche LLP

                                      II-1
   11

    24   Power of Attorney (included on signature page hereof)(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
   12

      (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.

                                      II-3
   13

                                   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
Registration Statement to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Seattle, State of Washington, on April 19, 2001.


                                        CRAY INC.


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

   14

      Each of the undersigned hereby constitutes and appoints James E. Rottsolk
and Burton J. Smith, and each of them, the undersigned's true and lawful
attorney-in-fact and agent, with full power of substitution, for the undersigned
and in his or her name, place and stead, in any and all capacities, to sign any
or all amendments or post-effective amendments to this Registration Statement,
and any other instruments or documents that said attorneys-in-fact and agents
may deem necessary or advisable, to enable Cray Inc. to comply with the
Securities Act of 1933, as amended, and any requirements of the Securities and
Exchange Commission in respect thereof, and to file the same, with all exhibits
thereto, with the Securities and Exchange Commission, granting unto said
attorneys-in-fact and agents and each of them full power and authority to do and
perform each and every act and thing requisite and necessary to be done, as
fully to all intents and purposes as the undersigned might or could do in
person, hereby ratifying and confirming all that each such attorney-in-fact and
agent, or his substitute, may lawfully do or cause to be done by virtue hereof.


      Pursuant to the requirements of the Securities Act of 1933, as amended,
this Registration Statement has been signed by the following persons in the
capacities indicated below on the 19th day of April, 2001:


Signature and Title


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

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

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