WHOLE FOODS MARKET INC
424B3, 1998-06-03
GROCERY STORES
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<PAGE>
 
PROSPECTUS SUPPLEMENT (dated June 3, 1998)
To Prospectus dated May 26, 1998

     The "Selling Holders" section of the Prospectus is amended to read as
follows:

                                SELLING HOLDERS

     The Debentures were originally issued by the Company and resold by BT Alex.
Brown Incorporated and Morgan Stanley & Co. Incorporated (the "Initial
Purchasers"), in transactions exempt from the registration requirements of the
Securities Act, to persons reasonably believed by the Initial Purchasers to be
"qualified institutional buyers" ("QIBs") as defined in Rule 144A under the
Securities Act, in compliance with Rule 144A under the Securities Act.  Such
persons constitute the "Selling Holders."  The Selling Holders (which term
includes their transferees, pledgees, donees or their successors) may from time
to time offer and sell pursuant to this Prospectus any or all of the Debentures
and Common Stock issued upon conversion of the Debentures.

     The following table sets forth information with respect to the Selling
Holders and the respective principal amounts of Debentures and shares of Common
Stock beneficially owned by each Selling Holder.  Such information has been
obtained from the Selling Holders.  Except as otherwise disclosed herein, none
of the Selling Holders has, or within the past three years has had, any position
office or other material relationship with the Company or any of its
predecessors or affiliates.  Because the Selling Holders may offer all or some
portion of the Debentures or the Common Stock issuable upon conversion thereof
pursuant to this Prospectus, no estimate can be given as to the amount of the
Debentures or the Common Stock issuable upon conversion thereof that will be
held by the Selling Holders upon termination at any such sales.  In addition,
the Selling Holders identified below may have sold, transferred or otherwise
disposed of all or a portion of their Debentures, since the date on which they
provided the information regarding their Debentures, in transactions exempt from
the registration requirements of the Securities Act.


<TABLE>
<CAPTION>
 
                                                PRINCIPAL AMOUNT OF           NUMBER OF SHARES
                                           DEBENTURES BENEFICIALLY OWNED       OF COMMON STOCK
         SELLING HOLDER                    AND THAT MAY BE OFFERED HEREBY   BENEFICIALLY OWNED (1)
- ----------------------------------------  -------------------------------  -----------------------
<S>                                        <C>                             <C>
Alexandra Global Investment Fund 1, Ltd.              $9,200,000                    ---
Associated Electric & Gas Insurance
 Services Limited                                        600,000                    ---
Baptist Health                                           282,000                    ---
Boston Museum of Fine Art                                141,000                    ---
BS Debt Income Fund C Class A                             40,000                    ---
BT Alex. Brown                                        27,072,000                    ---
CALAMOS Convertible Fund                               7,805,000                    ---
CALAMOS Global Growth and Income Fund                    490,000                    ---
CALAMOS Growth and Income Fund                         1,360,000                    ---
Carrigaholt Capital (Bermuda) L.P.                     4,250,000                    ---
CFW-C, L.P.                                           10,000,000                    ---
Champion International Corporation
 Master Retirement Trust                               6,685,000                    ---
Class IC Company, Ltd., The                            4,250,000                    ---
Delaware Group Premium Fund, Inc.                        300,000                    ---
Delta Airlines Master Trust                           11,400,000                    ---
Deutsche Bank AG                                      21,250,000                    ---
Dorinco Reinsurance Company                            2,800,000                    ---

</TABLE> 
<PAGE>
 
<TABLE>
<CAPTION>
 
                                                PRINCIPAL AMOUNT OF           NUMBER OF SHARES
                                           DEBENTURES BENEFICIALLY OWNED       OF COMMON STOCK
         SELLING HOLDER                    AND THAT MAY BE OFFERED HEREBY   BENEFICIALLY OWNED (1)
- ----------------------------------------  -------------------------------  -----------------------
<S>                                        <C>                             <C>
Dow Chemical Company Employees'
 Retirement Plan                                      11,490,000                    ---
Dunham & Assoc. Fund III                                  53,000                    ---
Dunham & Assoc. Fund II                                   99,000                    ---
Engineers Joint Pension Fund                             518,000                    ---
Fondren Foundation, The                                  470,000                    ---
Genesee County Employees' Retirement
 System                                                1,200,000                    ---
GPZ Trading LLC                                        2,000,000                    ---
Hamilton Global Investors Limited                     29,500,000                    ---
Hamilton Partners Limited
HBK Cayman L.P.                                        1,200,000                    ---
HBK Finance, L.P.                                      3,410,000                    ---
HBK Offshore Fund Ltd.                                 2,800,000                    ---
HBK Securities Ltd.                                    6,530,000                    ---
Highbridge Capital Corporation                        11,000,000                    ---
Kettering Medical Center Funded
 Depreciation Account                                    535,000                    ---
McMahan Securities Company, L.P.                         200,000                    ---
Nicholas Applegate Income & Growth Fund                4,935,000                    ---
Paloma Securities L.L.C.                               8,400,000                    ---
Port Authority of Allegheny County
 Retirement and Disability Allowance                   8,150,000                    ---
 Plan for the Employees Represented by
 Local 85 of the Amalgamated Transit
 Union
R2 Investments, LDC                                    4,850,000                    ---
Raytheon Company Master Pension Trust                  2,500,000                    ---
RJR Nabisco, Inc. Defined Benefit Master
 Trust                                                 5,205,000                    ---
San Diego City Retirement                              1,395,000                    ---
San Diego County Convertibles                          4,273,000                    ---
SBC Warburg Dillon Reed                                  800,000                    ---
Silverton International Fund Limited                   5,200,000                    ---
Societe Generale                                      11,000,000                    ---
Southern Farm Bureau Life Insurance
 Company                                               4,000,000                    ---
SPT                                                    4,300,000                    ---
Teachers Insurance and Annuity
 Association of America                               13,400,000                    ---
TQA Leverage Fund, L.P.                                1,000,000                    ---
TQA Vantage Fund, Ltd.                                 2,000,000                    ---
TQA Vantage Plus Ltd.                                  1,000,000                    ---
UBS Asset Management (New York)                        6,000,000                    ---
Unifi, Inc. Profit Sharing Plan and Trust              1,080,000                    ---
Univar Corporation                                     2,150,000                    ---
Van Kampen American Capital Harbor
 Fund(2)                                              16,019,009                    ---
Van Kampen American Capital Convertible
 Securities Fund(2)                                    2,781,000                    ---
Wake Forest University                                 1,104,000                    ---
</TABLE>

____________________
(1)  Does not include shares of Common Stock issuable upon conversion of
     Debentures.
(2)  Van Kampen American Capital Asset Management (the "Advisor") acts as
     investment advisor or sub-advisor to the funds indicated.  The Advisor has
     discretionary authority to make investment decisions with respect to the
     portfolios of the funds.  In addition, the security holder is an affiliate
     of Morgan Stanley & Co. Incorporated, an Initial Purchaser.


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