1

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

                                                  Registration No. 333-57972


                       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.

                        5,139,408 shares of common stock

        These shares of common stock are issuable upon exercise of common stock
purchase warrants owned by the selling shareholder listed on page 3 and are
being offered and sold from time to time by him.

        The selling securityholder 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. 333-57954, for the resale of 500,000
shares of common stock held by another shareholder, and the resale of these
500,000 shares of common stock 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 June 21, 1999, we issued a warrant to Terren S. Peizer in exchange
for $200,000. The warrant, which fully vested on June 21, 2001, is exercisable
for 5,139,408 shares of our common stock at an exercise price of $2.53 per share
and expires on June 21, 2009. The exercise price will be proportionately
adjusted for any split in the outstanding shares of our common stock or a
dividend on our common stock which is paid in common stock.

        The issuance of the warrant to Mr. Peizer is described more fully in our
current report on Form 8-K for the event of June 21, 1999, as filed with the
Securities and Exchange Commission on June 30, 1999.

        As of July 18, 2001, Mr. Peizer held no shares of our common stock. The
shares covered by this prospectus include only the shares of common stock
issuable to Mr. Peizer upon the exercise of the warrant described above.
All of the shares covered by this prospectus are being sold for the account of
Mr. Peizer. As of July 18, 2001, we had 41,438,117 shares outstanding.





                                                            Ownership After Offering
                                                             if All Shares Offered
                           Shares                             in Offering Are Sold
                         Owned Before      Shares Being    --------------------------
Selling Shareholder     Offering(1)(2)        Offered         Shares        Percent
-------------------   ----------------     ------------    ----------     -----------
                                                   
Terren S. Peizer            - 0 -           5,139,408        - 0 -            n/a



(1)  Does not include 5,139,408 shares issuable upon exercise of a warrant
     exercisable within 60 days of July 27, 2001.

(2)  Does not include 12,000 shares issuable upon exercise of options
     exercisable within 60 days of July 27, 2001.

        Mr. Peizer served as the chairman of our board of directors from
June 25, 1999 to December 21, 2000. Mr. Peizer continues to serve as a director
of Cray.

        Because Mr. Peizer may wish to be legally permitted to sell his shares
at any time he considers appropriate, we have agreed with Mr. Peizer 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 issuable upon exercise of the warrant, 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 issuable upon exercise of the warrant are no longer required to be
registered for sale by Mr. Peizer.



                                      -3-
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                              PLAN OF DISTRIBUTION

        Cray is registering the shares covered by this prospectus for Mr.
Peizer. Mr. Peizer or his pledgees, donees, transferees or other successors in
interest may sell the shares in the over-the-counter market or in other
transactions, 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:


        o       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;

        o       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


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

        Cray will pay the costs and fees of registering the shares, but Mr.
Peizer will pay any brokerage commissions, discounts or other expenses relating
to the sale of the shares. Cray and Mr. Peizer 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. Mr. Peizer 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 Mr. Peizer and may affect the marketability of
our common stock.

        Mr. Peizer may negotiate and pay brokers or dealers commissions,
discounts or concessions for their services. In making sales, brokers or dealers
engaged by Mr. Peizer may allow other broker or dealers to participate. However,
Mr. Peizer 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. In addition, the brokers' or dealers' commissions,
discounts or concessions may qualify as underwriters' compensation under the
Securities Act of 1933. If Mr. Peizer qualifies as an underwriter, he will be
subject to the prospectus delivery requirements of section 5(b)(2) of the
Securities Act of 1933.

        Mr. Peizer may also:

        o       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;

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



                                      -4-
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        o       sell his 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 Mr. Peizer 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 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.



                                      -5-
   8


         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

        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.



                                      -6-
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        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 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-
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                                     PART II

                   INFORMATION NOT REQUIRED IN THE PROSPECTUS

Item 14.    Other Expenses of Issuance and Distribution.

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

        SEC Registration fee.............................     $3,251

        Legal fees.......................................     $5,000

        Accountant's Fees................................     $2,500

        Miscellaneous....................................     $2,249

        Total............................................     $13,000
                                                              =======


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.


                                      II-1
   11

Item 16        Exhibits.

        4.1    Form of Warrant issued to Terren S. Peizer(1)


        5      Opinion on Legality


        23     Consent of Deloitte & Touche LLP


        24     Power of Attorney(1)


------------
(1)  Incorporated by reference to the Company's Registration Statement on
     Form S-3 Registration No. 333-57972, 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.


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        (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.

        (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-2E>
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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. 333-57972 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. 333-57972 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