WHOLE FOODS MARKET INC
10-K/A, 1999-02-10
GROCERY STORES
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<PAGE>
 
                                  Form 10-K/A

                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C.  20549

[x]  Annual report pursuant to Section 13 or 15(d) of the Securities Exchange
     Act of 1934 for fiscal year ended September 27, 1998; or
[ ]  Transition report pursuant to Section 13 or 15 (d) of the Securities
     Exchange Act of 1934 for the transition period from _____________ to
     ________________.

Commission file number:  0-19797

                           WHOLE FOODS MARKET, INC.
            (Exact name of registrant as specified in its charter)

  Texas                                                       74-1989366
 (State of                                                 (IRS employment
incorporation)                                           identification no.)

       601 North Lamar Street
             Suite 300
           Austin, Texas                                         78703
(Address of principal executive offices)                      (Zip Code)

              Registrant's telephone number, including area code:
                                 512-477-4455

          Securities registered pursuant to Section 12(b) of the Act:
                                     None

          Securities registered pursuant to section 12(g) of the Act:
                          Common Stock, no par value

                 $307,807,000 Principal Amount At Maturity of
           Zero Coupon Convertible Subordinated Debentures Due 2018

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the  preceding 12 months (or for such  shorter  period that the
registrant  was required  to file  such  reports), and  (2) has  been  subject
to such  filing requirements for the past 90 days. Yes x No

     Indicate by check mark if disclosure of delinquent  filers  pursuant to
Item 405 of Regulation  S-K is not contained  herein,  and will not be
contained,  to the best of registrant's knowledge,  in definitive proxy or
information  statements incorporated by reference in Part III of this Form 10-K
or any amendment to this Form 10-K. [ ]
<PAGE>
 
The aggregate market value of the voting stock held by non-affiliates of the
registrant on November 30, 1998 was approximately $1.2 billion.

The number of shares of the registrant's common stock, no par value, outstanding
as of November 30, 1998 was approximately 26,555,000.

The following document is incorporated by reference into the part of this annual
report on Form 10-K as indicated: None

                                       2
<PAGE>
 
                                   SIGNATURE


     Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this amendment to this report to be signed on its
behalf by the undersigned hereunto duly authorized.


                                WHOLE FOODS MARKET, INC.



Date: February 10, 1999         By: /s/ GLENDA FLANAGAN
                                   ----------------------------------------
                                   Glenda Flanagan, Chief Financial Officer

                                       3
<PAGE>
 
                               INDEX TO EXHIBITS
                               -----------------

Exhibits
- --------

  2.1  Agreement and Plan of Merger, among the Registrant, WFM Colorado
       Acquisition, Inc., Allegro Coffee Company, Inc. and the shareholders of
       Allegro Coffee Company, Inc. (4)

  2.2  Agreement and Plan of Merger, among the Inc., the Merchant of Vino
       companies,  and the  Registrant,  Whole Foods Market Group, stockholders
       of the Merchant of Vino Companies. (4)

  3.1  Restated Articles of Incorporation of the Registrant, as amended (2)

  3.2  By-laws of the Registrant adopted May 23, 1995 (8)

  4.1  Form of Zero Coupon Convertible Subordinated Debentures Due 2018. (5)

  4.2  Indentures between the Company and Chase Bank of Texas, National
       Association, as Trustee. (5)

  4.3  Registration Rights Agreement by and among the Company and BT Alex
       Brown Incorporated and Morgan Stanley & Co. Incorporated. (5)

 10.1  1987 Stock Option and Incentive Plan for Employees (3)

 10.2  1987 Stock Option Plan for Outside Directors (3)

 10.3  1993 Team Member Stock Ownership Plan (1)

 10.5  Form of Retention Agreement between the executive officers of the
       Registrant and the Registrant (3)

 10.6  Form of amendment to Retention Agreement (1)

 10.7  Amended and Restated Loan Agreement, dated December 27, 1994, by
       and among the Registrant, the subsidiaries of the Registrant and Texas
       Commerce Bank National Association (8)

 10.8  First Amendment dated May 16, 1996 to Amended and Restated Loan
       Agreement, dated December 27, 1994, by and among Registrant, the
       subsidiaries of the Registrant and Texas Commerce Bank National
       Association (9)

 10.9  Second Amendment dated December 24, 1996 to Amended and Restated
       Loan Agreement, dated December 27, 1994, by and among Registrant, the
       subsidiaries of the Registrant and Texas Commerce Bank National
       Association (10)

                                      E-1
<PAGE>
 
 10.10  Third Amendment dated March 24, 1997 to Amended and Restated Loan
        Agreement, dated December 27, 1994, by and among Registrant, the
        subsidiaries of the Registrant and Texas Commerce Bank National
        Association (10)

 10.11  Fourth Amendment dated September 2, 1997 to Amended and Restated
        Loan Agreement, dated December 27, 1994, by and among Registrant, the
        subsidiaries of the Registrant and Texas Commerce Bank National
        Association (10)

 10.12  Fifth Amendment dated December 19, 1997 to Amended and Restated
        Loan Agreement, dated December 27, 1994, by and among Registrant, the
        subsidiaries of the Registrant and Texas Commerce Bank National
        Association (11)

 10.13  1992 Stock Option Plan for Team Members, as amended (1)

 10.14  1992 Stock Option Plan for Outside Directors (1)

 10.15  1993 Team Member Stock Purchase Plan (1)

 10.16  Second Amended and Restated 1991 Stock Incentive Plan of Fresh Fields
        Markets, Inc. with amendments thereto (6)

 10.17  1994 Director Stock Option Plan with amendments thereto (6)

 10.18  Non-Qualified Stock Option Plan of Amrion, Inc. (7)

 10.19  1994 Non-Employee Director Stock Option Plan of Amrion, Inc. (7)

 12.1   Computation of Ratio of Earnings to Fixed Charges (12)

 21.1   Subsidiaries of the Registrant (11)

 23.1   Consent of KPMG Peat Marwick LLP (11)

 27.1   Financial Data Schedule (11)
- --------------------
(1)  Filed as an exhibit to Registration Statement on Form S-4 (No. 33-63824)
     and incorporated herein by reference.
(2)  Filed as an exhibit to Registration Statement on Form S-3 (No.33-69362) and
     incorporated herein by reference.
(3)  Filed as an exhibit to Registration Statement on Form S-1 (No. 33-44214)
     and incorporated herein by reference.
(4)  Filed as an exhibit to Registration Statement on Form S-3 (No. 333-43555)
     and incorporated herein by reference.
(5)  Filed as an exhibit to Registration Statement on Form S-3 (No. 333-51419)
     and incorporated herein by reference.

                                      E-2
<PAGE>
 
(6)  Filed as an exhibit to Registration Statement on Form S-8 (No. 33-11273)
     and incorporated herein by reference.
(7)  Filed as an exhibit to Registration Statement on Form S-8 (No. 33-35809)
     and incorporated herein by reference.
(8)  Filed as an exhibit to Registrant's Form 10-K for year ended September 24,
     1995 and incorporated herein by reference.
(9)  Filed as an exhibit to Registrant's Form 10-K for year ended September 29,
     1996 and incorporated herein by reference.
(10) Filed as an exhibit to Registrant's Form 10-K for year ended September 28,
     1997 and incorporated herein by reference.
(11) Previously filed.
(12) Filed herewith

                                      E-3

<PAGE>
 
                                                                    Exhibit 12.1
                                                                    ------------

Whole Foods Market, Inc.  and Subsidiaries
Computation of Ratio of Earnings to Fixed Charges


<TABLE>
<CAPTION>
                                                                        Fiscal Year End (1)
                                                             Sep 27   Sep 28   Sep 29   Sep 24  Sep 25
                                                              1998     1997     1996     1995    1994
                                                              ----     ----     ----     ----    ----
<S>                                                          <C>      <C>     <C>       <C>     <C>
Earnings:                                               
     Income (loss) before income taxes                       $72,056  39,368  (14,119)  11,083   8,867
     Interest expense                                          7,685   6,044    4,671    2,368     127
     Rental expense representative of interest                11,727   9,620    8,145    6,370   4,795
                                                             -------  ------  -------   ------  ------
          Total available earnings                            91,468  55,032   (1,303)  19,821  13,789
                                                             -------  ------  -------   ------  ------
                                                                                                      
Fixed charges                                                                                         
     Interest, including capitalized interest                  8,420   6,814    5,854    3,177     499
     Rental expense representative of interest                11,727   9,620    8,145    6,370   4,795
                                                             -------  ------  -------   ------  ------
          Total fixed charges                                $20,147  16,434   13,999    9,547   5,294
                                                             -------  ------  -------   ------  ------
                                                        
Ratio of available earnings to fixed charges (2)               4.54x   3.35x       --    2.08x   2.60x
                                                             =======  ======  =======   ======  ======
</TABLE>

(1)  Fiscal years 1998, 1997, 1995 and 1994 are 52-week years and fiscal year
     1996 is a 53-week year.

(2)  For the fiscal year ended September 29, 1996, earnings were inadequate to
     cover fixed charges in the amount of $15.3 million.


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