10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C.  20549

FORM 10-Q

xQuarterly report pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

for the period ended April 10, 2011;

or

oTransition 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 employer
incorporation)	identification no.)

550 Bowie St.

Austin, Texas 78703

(Address of principal executive offices)

512-477-4455

(Registrant’s telephone number, including area code)

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 o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes x No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company (as defined in Rule 12b-2 of the Exchange Act).

Large accelerated filer x	Accelerated filer o
Non-accelerated filer o	Smaller reporting company o
(Do not check if a smaller reporting company)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act.) Yes o No x

The number of shares of the registrant’s common stock, no par value, outstanding as of April 10, 2011 was 175,712,740 shares.

Whole Foods Market, Inc.

Form 10-Q

Table of Contents

	Page
	Number
Part I. Financial Information
Item 1. Financial Statements
Consolidated Balance Sheets (unaudited), April 10, 2011 and September 26, 2010	3
Consolidated Statements of Operations (unaudited), for the twelve and twenty-eight weeks ended April 10, 2011 and April 11, 2010	4
Consolidated Statements of Shareholders’ Equity and Comprehensive Income (unaudited), for the twenty-eight weeks ended April 10, 2011 and fiscal year ended September 26, 2010	5
Consolidated Statements of Cash Flows (unaudited), for the twenty-eight weeks ended April 10, 2011 and April 11, 2010	6
Notes to Consolidated Financial Statements (unaudited)	7
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations	12
Item 4. Controls and Procedures	17
Part II. Other Information
Item 1. Legal Proceedings	18
Item 6. Exhibits	18
Signature	19

2

Part I. Financial Information

Item 1. Financial Statements

Whole Foods Market, Inc.

Consolidated Balance Sheets (unaudited)

April 10, 2011 and September 26, 2010

(In thousands)

	2011		2010
Assets
Current assets:
Cash and cash equivalents	$	162,103	$	131,996
Short-term investments — available-for-sale securities	391,846		329,738
Restricted cash	86,785		86,802
Accounts receivable	155,092		133,346
Merchandise inventories	341,539		323,487
Prepaid expenses and other current assets	62,127		54,686
Deferred income taxes	103,394		101,464
Total current assets	1,302,886		1,161,519
Property and equipment, net of accumulated depreciation and amortization	1,933,764		1,886,130
Long-term investments — available-for-sale securities	80,437		96,146
Goodwill	661,483		665,224
Intangible assets, net of accumulated amortization	67,093		69,064
Deferred income taxes	81,549		99,156
Other assets	9,362		9,301
Total assets	$	4,136,574	$	3,986,540
Liabilities and Shareholders’ Equity
Current liabilities:
Current installments of long-term debt and capital lease obligations	$	435	$	410
Accounts payable	233,991		213,212
Accrued payroll, bonus and other benefits due team members	254,334		244,427
Dividends payable	17,572		—
Other current liabilities	338,072		289,823
Total current liabilities	844,404		747,872
Long-term debt and capital lease obligations, less current installments	207,741		508,288
Deferred lease liabilities	321,986		294,291
Other long-term liabilities	59,708		62,831
Total liabilities	1,433,839		1,613,282
Shareholders’ equity:
Common stock, no par value, 300,000 shares authorized; 175,713 and 172,033 shares issued and outstanding at 2011 and 2010, respectively	1,954,250		1,773,897
Accumulated other comprehensive income	6,408		791
Retained earnings	742,077		598,570
Total shareholders’ equity	2,702,735		2,373,258
Commitments and contingencies
Total liabilities and shareholders’ equity	$	4,136,574	$	3,986,540

The accompanying notes are an integral part of these consolidated financial statements.

3

Whole Foods Market, Inc.

Consolidated Statements of Operations (unaudited)

(In thousands, except per share amounts)

	Twelve weeks ended						Twenty-eight weeks ended
	April 10,			April 11,			April 10,			April 11,
	2011			2010			2011			2010
Sales	$	2,350,518		$	2,106,061		$	5,354,173		$	4,745,219
Cost of goods sold and occupancy costs	1,513,699			1,363,632			3,479,115			3,096,574
Gross profit	836,819			742,429			1,875,058			1,648,645
Direct store expenses	608,484			551,705			1,398,867			1,254,511
General and administrative expenses	75,661			62,540			164,172			138,476
Pre-opening expenses	9,543			11,636			18,183			24,445
Relocation, store closure and lease termination costs	1,003			(2,688		)	4,149			9,724
Operating income	142,128			119,236			289,687			221,489
Interest expense	(1,283		)	(7,783		)	(3,616		)	(18,336		)
Investment and other income	1,941			1,910			4,593			3,693
Income before income taxes	142,786			113,363			290,664			206,846
Provision for income taxes	52,851			45,912			111,999			84,240
Net income	89,935			67,451			178,665			122,606
Preferred stock dividends	—			—			—			5,478
Income available to common shareholders	$	89,935		$	67,451		$	178,665		$	117,128
Basic earnings per share	$	0.51		$	0.39		$	1.03		$	0.73
Weighted average shares outstanding	174,686			170,893			173,606			161,476
Diluted earnings per share	$	0.51		$	0.39		$	1.02		$	0.72
Weighted average shares outstanding, diluted basis	177,124			171,826			175,614			170,953
Dividends declared per common share	$	0.10		$	—		$	0.20		$	—

The accompanying notes are an integral part of these consolidated financial statements.

4

Whole Foods Market, Inc.

Consolidated Statements of Shareholders’ Equity and Comprehensive Income (unaudited)

Twenty-eight weeks ended April 10, 2011 and fiscal year ended September 26, 2010

(In thousands)

					Accumulated
					other						Total
	Shares		Common		comprehensive			Retained			shareholders’
	outstanding		stock		income (loss)			earnings			equity
Balances at September 27, 2009	140,542		$	1,283,028	$	(13,367	)	$	358,215		$	1,627,876
Net income	—		—		—			245,833			245,833
Foreign currency translation adjustments, net	—		—		1,564			—			1,564
Reclassification adjustments for amounts included in income	—		—		12,943			—			12,943
Change in unrealized losses, net of income taxes	—		—		(349		)	—			(349		)
Comprehensive income											259,991
Redeemable preferred stock dividends	358		5,195		—			(5,478		)	(283		)
Conversion of preferred stock	29,311		413,052		—			—			413,052
Issuance of common stock pursuant to team member stock plans	1,822		47,020		—			—			47,020
Excess tax benefit related to exercise of team member stock options	—		2,708		—			—			2,708
Share-based payment expense	—		22,894		—			—			22,894
Balances at September 26, 2010	172,033		1,773,897		791			598,570			2,373,258
Net income	—		—		—			178,665			178,665
Foreign currency translation adjustments, net	—		—		5,389			—			5,389
Reclassification adjustments for amounts included in income	—		—		245			—			245
Change in unrealized losses, net of income taxes	—		—		(17		)	—			(17		)
Comprehensive income											184,282
Dividends ($0.20 per common share)	—		—		—			(34,920		)	(34,920		)
Issuance of common stock pursuant to team member stock plans	3,684		154,968		—			—			154,968
Excess tax benefit related to exercise of team member stock options	—		12,537		—			—			12,537
Share-based payment expense	—		12,848		—			—			12,848
Other	(4	)	—		—			(238		)	(238		)
Balances at April 10, 2011	175,713		$	1,954,250	$	6,408		$	742,077		$	2,702,735

The accompanying notes are an integral part of these consolidated financial statements.

5

Whole Foods Market, Inc.

Consolidated Statements of Cash Flows (unaudited)

(In thousands)

	Twenty-eight weeks ended
	April 10,			April 11,
	2011			2010
Cash flows from operating activities
Net income	$	178,665		$	122,606
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization	152,903			146,795
Loss (gain) on disposition of fixed assets	914			(2,172		)
Impairment of long-lived assets	581			1,875
Share-based payment expense	12,848			9,173
LIFO expense (benefit)	3,000			(2,805		)
Deferred income tax expense (benefit)	15,747			(7,773		)
Excess tax benefit related to exercise of team member stock options	(9,251		)	(1,844		)
Deferred lease liabilities	24,110			19,954
Other	(379		)	(3,895		)
Net change in current assets and liabilities:
Accounts receivable	(24,991		)	(17,581		)
Merchandise inventories	(20,474		)	(2,734		)
Prepaid expenses and other current assets	(7,310		)	10,370
Accounts payable	20,176			17,565
Accrued payroll, bonus and other benefits due team members	9,580			14,980
Other current liabilities	46,457			33,342
Net change in other long-term liabilities	241			5,127
Net cash provided by operating activities	402,817			342,983
Cash flows from investing activities
Development costs of new locations	(89,451		)	(110,966		)
Other property and equipment expenditures	(80,130		)	(36,055		)
Purchase of available-for-sale securities	(780,154		)	(615,492		)
Sale of available-for-sale securities	731,306			192,685
Decrease (increase) in restricted cash	17			(16,184		)
Other investing activities	(1,576		)	(1,048		)
Net cash used in investing activities	(219,988		)	(587,060		)
Cash flows from financing activities
Common stock dividends paid	(17,348		)	—
Preferred stock dividends paid	—			(8,500		)
Issuance of common stock	153,067			34,321
Excess tax benefit related to exercise of team member stock options	9,251			1,844
Payments on long-term debt and capital lease obligations	(300,123		)	(110		)
Net cash provided by (used in) financing activities	(155,153		)	27,555
Effect of exchange rate changes on cash and cash equivalents	2,431			1,601
Net change in cash and cash equivalents	30,107			(214,921		)
Cash and cash equivalents at beginning of period	131,996			430,130
Cash and cash equivalents at end of period	$	162,103		$	215,209
Supplemental disclosures of cash flow information:
Interest paid	$	14,002		$	28,653
Federal and state income taxes paid	$	109,611		$	78,616
Non-cash transaction:
Conversion of redeemable preferred stock into common stock	$	—		$	418,247

The accompanying notes are an integral part of these consolidated financial statements.

6

Whole Foods Market, Inc.

Notes to Consolidated Financial Statements (unaudited)

April 10, 2011

(1) Basis of Presentation

The accompanying unaudited consolidated financial statements of Whole Foods Market, Inc. and its consolidated subsidiaries (collectively “Whole Foods Market,” “Company,” or “We”) have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial statements and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. The information included in this Form 10-Q should be read in conjunction with Management’s Discussion and Analysis, the consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 26, 2010. In the opinion of management, the accompanying consolidated financial statements reflect all adjustments, consisting of normal recurring accruals, considered necessary for a fair presentation. Interim results are not necessarily indicative of results for any other interim period or for a full fiscal year. The Company reports its results of operations on a fifty-two or fifty-three week fiscal year ending on the last Sunday in September. The first fiscal quarter is sixteen weeks, the second and third quarters each are twelve weeks, and the fourth quarter is twelve or thirteen weeks. Fiscal years 2011 and 2010 are fifty-two week fiscal years. We have one operating segment and a single reportable segment, natural and organic foods supermarkets. The following is a summary of percentage sales by geographic area for the twelve and twenty-eight weeks ended:

	April 10,		April 11,
	2011		2010
Sales:
United States	96.9	%	97.0	%
Canada and United Kingdom	3.1		3.0
Total sales	100.0	%	100.0	%

The following is a summary of the percentage of net long-lived assets by geographic area as of the dates indicated:

	April 10,		September 26,
	2011		2010
Long-lived assets, net:
United States	96.2	%	96.6	%
Canada and United Kingdom	3.8		3.4
Total long-lived assets, net	100.0	%	100.0	%

(2) Recent Accounting Pronouncements

In December 2010, the Financial Accounting Standards Board (“FASB”) issued amended guidance within Accounting Standards Codification (“ASC”) 805, “Business Combinations,” which updates previous guidance on this topic and applies to all material transactions. The amendments specify that if a public entity presents comparative financial statements, the entity should disclose revenue and earnings of the combined entity as though the business combination(s) had occurred as of the beginning of the comparable prior annual reporting period only. Additional amendments expand supplemental pro forma disclosures to include a description of the nature and amount of material, nonrecurring pro forma adjustments directly attributable to the business combination included in the reported pro forma revenue and earnings. The updated guidance is effective for fiscal years beginning after December 15, 2010 and is applied prospectively to business combinations completed on or after that date. The provisions are effective for the Company’s fiscal year ending September 30, 2012. We do not expect the adoption of these provisions to have a significant effect on our consolidated financial statements.

In May 2011, the FASB issued Accounting Standards Update (“ASU”) 2011-04, “Amendments to Achieve Common Fair Value Measurement and Disclosure Requirements in U.S. GAAP and IFRSs,” which amends ASC 820, “Fair Value Measurement.” The amended guidance changes the wording used to describe many requirements in U.S. GAAP for measuring fair value and for disclosing information about fair value measurements. Additionally, the amendments clarify the FASB’s intent about the application of existing fair value measurement requirements. The guidance provided in ASU No. 2011-04 is effective for interim and annual periods beginning after December 15, 2011 and is applied prospectively. The provisions are effective for the Company’s second quarter of fiscal year ending September 30, 2012. We do not expect the adoption of these provisions to have a significant effect on our consolidated financial statements.

7

(3) Fair Value Measurements

Assets Measured at Fair Value on a Recurring Basis

The Company holds money market fund investments that are classified as either cash equivalents or restricted cash and available-for-sale marketable securities generally consisting of state and local government obligations that are measured at fair value on a recurring basis, based on current market prices. Currently, the Company primarily holds variable rate demand notes. At April 10, 2011, the average effective maturity of the Company’s short and long-term investments was approximately three and 15 months, respectively.

The Company held the following financial assets at fair value, based on the hierarchy input levels indicated, on a recurring basis (in thousands):

April 10, 2011	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Assets:
Money market fund investments	$	119,426	$	—	$	—	$	119,426
Marketable securities — available-for-sale	472,283		—		—		472,283
Total	$	591,709	$	—	$	—	$	591,709

September 26, 2010	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Assets:
Money market fund investments	$	112,363	$	—	$	—	$	112,363
Marketable securities — available-for-sale	425,884		—		—		425,884
Total	$	538,247	$	—	$	—	$	538,247

(4) Goodwill and Other Intangible Assets

There were no impairments of goodwill during the twenty-eight weeks ended April 10, 2011 or April 11, 2010. The Company recorded goodwill adjustments of approximately $3.7 million and $2.6 million, related to actual exit costs of certain restructuring reserves, during the twenty-eight weeks ended April 10, 2011 and April 11, 2010, respectively. The components of intangible assets were as follows (in thousands):

	April 10, 2011					September 26, 2010
	Gross carrying		Accumulated			Gross carrying		Accumulated
	amount		amortization			amount		amortization
Indefinite-lived contract-based	$	1,792	$	—		$	1,643	$	—
Definite-lived contract-based	96,776		(32,581		)	96,821		(30,706		)
Definite-lived marketing-related and other	1,307		(201		)	1,574		(268		)
	$	99,875	$	(32,782	)	$	100,038	$	(30,974	)

Amortization associated with intangible assets totaled approximately $2.0 million and $3.8 million for the twelve and twenty-eight weeks ended April 10, 2011, and approximately $1.3 million and $3.2 million, respectively, for the same periods of the prior fiscal year. Future amortization associated with the net carrying amount of intangible assets is estimated to be approximately as follows (in thousands):

Remainder of fiscal year 2011	$	2,674
Fiscal year 2012	5,268
Fiscal year 2013	4,997
Fiscal year 2014	4,887
Fiscal year 2015	4,550
Future fiscal years	42,925
	$	65,301

8

(5) Reserves for Closed Properties

Following is a summary of store closure reserve activity during the twenty-eight weeks ended April 10, 2011 and fiscal year ended September 26, 2010 (in thousands):

	April 10,			September 26,
	2011			2010
Beginning balance	$	59,298		$	69,228
Additions	2,059			5,236
Usage	(13,030		)	(19,431		)
Adjustments	(2,811		)	4,265
Ending balance	$	45,516		$	59,298

Additions to store closure reserves relate to the accretion of interest on existing reserves. Usage included approximately $7.7 million and $6.6 million in termination fees related to certain idle properties, and approximately $5.4 million and $12.8 million in ongoing cash rental payments during the twenty-eight weeks ended April 10, 2011 and fiscal year ended September 26, 2010, respectively. Additionally, the Company recorded goodwill adjustments of approximately $3.7 million during the twenty-eight weeks ended April 10, 2011.

(6) Long-Term Debt

The Company had a $700 million, five-year term loan agreement due in 2012, with outstanding balances of $190 million and $490 million at April 10, 2011 and September 26, 2010, respectively. Subsequent to the end of the second fiscal quarter, the Company repaid the remaining $190 million on the term loan. The Company’s obligations under the facility are secured by liens on certain of the Company’s assets, including stock of our subsidiaries. At April 10, 2011 we were in compliance with all applicable debt covenants.

The Company has outstanding a $350 million revolving line of credit that extends to 2012. The Company’s obligations under the facility are secured by liens on certain of the Company’s assets, including stock of our subsidiaries. At April 10, 2011 we were in compliance with all applicable debt covenants. At April 10, 2011 and September 26, 2010 the Company had no amounts drawn under this agreement. The amount available to the Company under the agreement was effectively reduced to approximately $342.9 million by outstanding letters of credit totaling approximately $7.1 million at April 10, 2011 and September 26, 2010.

During fiscal year 2008, the Company entered into an interest rate swap agreement, which expired in October 2010, with a notional amount of $490 million to effectively fix the interest rate on $490 million of the term loan at 4.718%, excluding the applicable margin and associated fees, to help manage cash flow exposure related to interest rate fluctuations. The interest rate swap was designated as a cash flow hedge. The carrying amount of the Company’s interest rate swap totaled approximately $0.4 million at September 26, 2010 and was included in the “Long-term debt and capital lease obligations, less current installments” line item on the Consolidated Balance Sheets. During the first quarter of fiscal year 2011 the Company had reclassified approximately $0.2 million from accumulated other comprehensive income related to ongoing interest payments that was included in the “Interest expense” line item on the Consolidated Statements of Operations. During the twelve and twenty-eight weeks ended April 11, 2010 the Company had reclassified approximately $3.0 million and $7.0 million, respectively, from accumulated other comprehensive income related to ongoing interest payments.

(7) Shareholders’ Equity

Dividends per Common Share

During the twelve weeks ended April 10, 2011, the Company’s Board of Directors declared a cash dividend to shareholders of $0.10 per common share, payable on April 22, 2011 to shareholders of record on April 12, 2011. Approximately $17.6 million was included in the “Dividends payable” line item on the Consolidated Balance Sheets at April 10, 2011.

Comprehensive Income

Our comprehensive income was comprised of: net income; unrealized gains and losses on investments; unrealized gains and losses on cash flow hedge instruments, including reclassification adjustments of unrealized losses to net income related to ongoing interest payments; and foreign currency translation adjustments, net of income taxes.

9

Comprehensive income was as follows (in thousands):

	Twelve weeks ended					Twenty-eight weeks ended
	April 10,		April 11,			April 10,			April 11,
	2011		2010			2011			2010
Net income	$	89,935	$	67,451		$	178,665		$	122,606
Foreign currency translation adjustments, net	3,139		(1,312		)	5,389			1,794
Reclassification adjustments for amounts included in net income	—		3,046			245			7,025
Unrealized gains / (losses), net	239		(183		)	(17		)	(633		)
Comprehensive income	$	93,313	$	69,002		$	184,282		$	130,792

At April 10, 2011, accumulated other comprehensive income primarily consisted of foreign currency translation adjustment gains of approximately $6.2 million. Unrealized losses on investments at April 10, 2011 and April 11, 2010 related to aggregate available-for-sale investments totaling approximately $111.9 million and $68.0 million, respectively.

(8) Earnings per Share

The computation of basic earnings per share is based on the number of weighted average common shares outstanding during the period. The computation of diluted earnings per share for the twelve and twenty-eight weeks ended April 10, 2011 and April 11, 2010 includes the dilutive effect of common stock equivalents consisting of incremental common shares deemed outstanding from the assumed exercise of stock options. Additionally, the computation of diluted earnings per share for the twenty-eight weeks ended April 11, 2010 includes the assumed conversion of Series A Preferred Stock.

A reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations follows (in thousands, except per share amounts):

	Twelve weeks ended				Twenty-eight weeks ended
	April 10,		April 11,		April 10,		April 11,
	2011		2010		2011		2010
Income available to common shareholders (numerator for basic earnings per share)	$	89,935	$	67,451	$	178,665	$	117,128
Preferred stock dividends	—		—		—		5,478
Adjusted income available to common shareholders (numerator for diluted earnings per share)	$	89,935	$	67,451	$	178,665	$	122,606
Weighted average common shares outstanding (denominator for basic earnings per share)	174,686		170,893		173,606		161,476
Potential common shares outstanding:
Incremental shares from assumed exercise of stock options	2,438		933		2,008		654
Assumed conversion of redeemable preferred stock	—		—		—		8,823
Weighted average common shares outstanding and potential additional common shares outstanding (denominator for diluted earnings per share)	177,124		171,826		175,614		170,953
Basic earnings per share	$	0.51	$	0.39	$	1.03	$	0.73
Diluted earnings per share	$	0.51	$	0.39	$	1.02	$	0.72

The computation of diluted earnings per share for the twelve and twenty-eight weeks ended April 10, 2011 does not include options to purchase approximately 4.9 million shares and 6.8 million shares of common stock due to their antidilutive effect. For the twelve and twenty-eight weeks ended April 11, 2010, the computation of diluted earnings per share does not include options to purchase approximately 12.2 million shares and 12.3 million shares of common stock, respectively, due to their antidilutive effect.

10

(9) Share-Based Payments

Total share-based payment expense before income taxes recognized during the twelve and twenty-eight weeks ended April 10, 2011 was approximately $5.5 million and $12.8 million, respectively, and approximately $3.9 million and $9.2 million, respectively, for the same periods of the prior fiscal year. Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 10,			April 11,			April 10,			April 11,
	2011			2010			2011			2010
Cost of goods sold and occupancy costs	$	288		$	165		$	658		$	385
Direct store expenses	2,894			2,265			6,619			5,295
General and administrative expenses	2,307			1,502			5,571			3,493
Share-based payment expense before income taxes	5,489			3,932			12,848			9,173
Income tax benefit	(1,999		)	(1,587		)	(4,870		)	(3,699		)
Net share-based payment expense	$	3,490		$	2,345		$	7,978		$	5,474

At April 10, 2011 and September 26, 2010, approximately 13.6 million shares and 12.7 million shares, respectively, of our common stock were available for future stock incentive grants. At April 10, 2011 and September 26, 2010, there was approximately $50.6 million and $62.2 million of unrecognized share-based payment expense, respectively, related to nonvested stock options, net of estimated forfeitures, related to approximately 5.8 million shares. We anticipate this expense to be recognized over a weighted average period of approximately three years.

(10) Commitments and Contingencies

The Company is exposed to claims and litigation matters arising in the ordinary course of business and uses various methods to resolve these matters in a manner that we believe best serves the interests of our stakeholders. Our primary contingencies are associated with insurance and self-insurance obligations and litigation matters. We use a combination of insurance and self-insurance plans to provide for the potential liabilities for workers’ compensation, general liability, property insurance, director and officers’ liability insurance, vehicle liability, and employee health care benefits. Estimation of our insurance and self-insurance liabilities requires significant judgments, and actual claim settlements and associated expenses may differ from our current provisions for loss. We have exposures to loss contingencies arising from pending or threatened litigation for which assessing and estimating the outcomes of these matters involve substantial uncertainties.

On October 27, 2008, Whole Foods Market was served with the complaint in Kottaras v. Whole Foods Market, Inc., a putative class action filed in the United States District Court for the District of Columbia, seeking treble damages, equitable, injunctive, and declaratory relief and alleging that the acquisition and merger between Whole Foods Market and Wild Oats violates various provisions of the federal antitrust laws. This case continues to be in the early stages of litigation. Whole Foods Market cannot at this time predict the likely outcome of this judicial proceeding or estimate the amount or range of loss or possible loss that may arise from it. The Company has not accrued any loss related to the outcome of this case as of April 10, 2011.

The Company evaluates contingencies on an ongoing basis and has established loss provisions for matters in which losses are probable and the amount of loss can be reasonably estimated. Insurance and legal settlement liabilities are included in the “Other current liabilities” line item on the Consolidated Balance Sheets. We believe the recorded reserves in our consolidated financial statements are adequate in light of the probable and estimable liabilities. However, resolution of contingencies resulting in amounts that vary materially from the Company’s current estimates could have a material adverse effect on the Company’s results of operations, cash flows, or financial condition.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

We wish to caution you that there are risks and uncertainties that could cause our actual results to be materially different from those indicated by forward-looking statements that we make from time to time in filings with the Securities and Exchange Commission (“SEC”), news releases, reports, proxy statements, registration statements and other written communications, as well as oral forward-looking statements made from time to time by representatives of our Company. These risks and uncertainties include those listed in the Company’s Annual Report on Form 10-K for the fiscal year ended September 26, 2010. These risks and uncertainties and additional risks and uncertainties not presently known to us or that we currently deem immaterial may cause our business, financial condition, operating results and cash flows to be materially adversely affected. Except for the historical information contained herein, the matters discussed in this analysis are forward-looking statements that involve risks and uncertainties, including general business conditions, changes in overall economic conditions that impact consumer spending, including fuel prices and housing market trends, the impact of competition, and other factors which are often beyond the control of the Company. The Company does not undertake any obligation to update forward-looking statements except as required by law.

General

Whole Foods Market, Inc. is the leading natural and organic foods supermarket and America’s first national “Certified Organic” grocer. Our Company mission is to promote the vitality and well-being of all individuals by supplying the highest quality, most wholesome foods available. Through our growth, we have had a significant and positive impact on the natural and organic foods movement throughout the United States, helping lead the industry to nationwide acceptance. As of April 10, 2011, we operated 304 stores: 293 stores in 38 U.S. states and the District of Columbia; six stores in Canada; and five stores in the United Kingdom. We have one operating segment, natural and organic foods supermarkets.

Our results of operations have been and may continue to be materially affected by the timing and number of new store openings. New stores generally become profitable during their first year of operation; although some new stores may incur operating losses for the first several years of operation. The Company’s average weekly sales are typically highest in the second and third fiscal quarters, and lowest in the fourth fiscal quarter. Gross profit is typically lower in the first fiscal quarter due to the product mix of holiday sales, and in the fourth fiscal quarter due to the seasonally slower sales in the summer months. Our gross profit may increase or decrease slightly depending on the mix of sales from new stores, seasonality, the impact of weather or a host of other factors, including inflation in product costs.

Sales of a store are deemed to be comparable commencing in the fifty-third full week after the store was opened or acquired. Stores acquired in purchase acquisitions enter the comparable store sales base effective the fifty-third full week following the date of the merger. Identical store sales exclude sales from relocated stores and remodeled stores with changes in square footage greater than 20% from the comparable calculation to reduce the impact of square footage growth on the comparison. Stores closed for eight or more days are excluded from the comparable and identical store base from the first fiscal week of closure until re-opened for a full fiscal week.

The Company reports its results of operations on a fifty-two or fifty-three week fiscal year ending on the last Sunday in September. Fiscal years 2011 and 2010 are fifty-two week years.

Economic and Industry Factors

Food retailing is a large, intensely competitive industry. Our competition varies across the Company and includes but is not limited to local, regional, national and international conventional and specialty supermarkets, natural foods stores, warehouse membership clubs, smaller specialty stores, farmers’ markets, and restaurants, each of which competes with us on the basis of store ambiance and experience, product selection, quality, customer service, price or a combination of these factors. Natural and organic food continues to be one of the fastest growing segments of food retailing today.

We believe our value efforts and differentiation continue to gain traction as evidenced by our strong 6.0% increase in transaction count in identical stores. As anticipated, the inflationary pressures on product costs accelerated in the twelve weeks ended April 10, 2011. A 1.5% percent increase in basket size during the second fiscal quarter was driven primarily by an increase in the average price per item, with only a slight increase in items per basket. We have worked very hard over the last couple of years to successfully improve our price image and remain focused on maintaining our relative price position in the marketplace. We are hopeful that we can again strike the right balance between rising product costs and our retails based on our contracts, distribution, and tools to manage value.

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Outlook for Fiscal Year 2011

The following table provides additional information on the Company’s results through April 10, 2011 and expectations for the remainder of fiscal year 2011:

		Implied
		third and fourth
	Twenty-eight weeks	quarter of	Estimated
	ended April 10, 2011	fiscal year 2011	fiscal year 2011
Sales growth	12.8%	10.3% – 12.4%	11.7% – 12.6%
Comparable store sales growth	8.5%	7.2% – 9.2%	7.9% – 8.9%
Identical store sales growth	8.5%	7.0% – 9.0%	7.8% – 8.7%
General and administrative expenses	3.1%	3.0%	3.0%
Pre-opening and relocation costs	$22 million	$28 – $31 million	$50 – $53 million
Tax rate	38.5%	38.5% – 39.0%	38.5 – 38.8%
Diluted earnings per share	$1.02	$0.85 – $0.88	$1.87 – $1.90
Capital expenditures	$170 million	$180 – $230 million	$350 – $400 million
Weighted square footage growth	6%	4%	5%

Results of Operations

The following table sets forth the Company’s statements of operations data expressed as a percentage of sales:

	Twelve weeks ended				Twenty-eight weeks ended
	April 10,		April 11,		April 10,		April 11,
	2011		2010		2011		2010
Sales	100.0	%	100.0	%	100.0	%	100.0	%
Cost of goods sold and occupancy costs	64.4		64.7		65.0		65.3
Gross profit	35.6		35.3		35.0		34.7
Direct store expenses	25.9		26.2		26.1		26.4
General and administrative expenses	3.2		3.0		3.1		2.9
Pre-opening expenses	0.4		0.6		0.3		0.5
Relocation, store closure and lease termination costs	—		(0.1	)	0.1		0.2
Operating income	6.0		5.7		5.4		4.7
Interest expense	(0.1	)	(0.4	)	(0.1	)	(0.4	)
Investment and other income	0.1		0.1		0.1		0.1
Income before income taxes	6.1		5.4		5.4		4.4
Provision for income taxes	2.2		2.2		2.1		1.8
Net income	3.8		3.2		3.3		2.6
Preferred stock dividends	—		—		—		0.1
Income available to common shareholders	3.8	%	3.2	%	3.3	%	2.5	%

Figures may not sum due to rounding.

Sales increased approximately 11.6% and 12.8% for the twelve and twenty-eight weeks ended April 10, 2011, respectively, over the same periods of the prior fiscal year. Comparable and identical store sales increased 7.8% and 8.5% for the twelve and twenty-eight weeks ended April 10, 2011, respectively, including a negative impact of 50 basis points from Easter shifting from the second fiscal quarter last year to the third fiscal quarter in the current year. As of April 10, 2011, there were 290 locations in the comparable store base. The number of stores open fifty-two weeks or less equaled 15 at April 10, 2011. The sales increase contributed by stores open less than fifty-two weeks totaled approximately $85.9 million and $178.2 million for the twelve and twenty-eight weeks ended April 10, 2011, respectively. Average weekly sales per store for all stores increased 7.4% to approximately $0.6 million, translating to sales per square foot of approximately $888.

Gross profit as a percentage of sales for the twelve and twenty-eight weeks ended April 10, 2011 was approximately 35.6% and 35.0%, respectively, compared to approximately 35.3% and 34.7%, respectively, for the same periods of the prior fiscal year. Factors contributing to the increases in gross profit as a percentage of sales include lower occupancy costs and cost of goods sold as a percentage of sales, offset by increases in LIFO expenses. For the twelve and twenty-eight weeks ended April 10, 2011, the Company recognized LIFO charges totaling approximately $1.0 million and $3.0 million, respectively, compared to LIFO credits of approximately $3.0 million and $2.8 million, respectively, for the same periods of the prior fiscal year.

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Direct store expenses as a percentage of sales for the twelve and twenty-eight weeks ended April 10, 2011 were approximately 25.9% and 26.1%, respectively, compared to approximately 26.2% and 26.4%, respectively, for the same periods of the prior fiscal year. The decreases in direct store expenses as a percentage of sales were due to leverage in wages, depreciation expense and healthcare costs as a percentage of sales.

General and administrative expenses as a percentage of sales for the twelve and twenty-eight weeks ended April 10, 2011 were approximately 3.2% and 3.1%, respectively, compared to approximately 3.0% and 2.9%, respectively, for the same periods of the prior fiscal year. The increase in general and administrative expenses as a percentage of sales is due primarily to an increase in salaries and benefits as a percentage of sales.

Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 10,			April 11,			April 10,			April 11,
	2011			2010			2011			2010
Cost of goods sold and occupancy costs	$	288		$	165		$	658		$	385
Direct store expenses	2,894			2,265			6,619			5,295
General and administrative expenses	2,307			1,502			5,571			3,493
Share-based payment expense before income taxes	5,489			3,932			12,848			9,173
Income tax benefit	(1,999		)	(1,587		)	(4,870		)	(3,699		)
Net share-based payment expense	$	3,490		$	2,345		$	7,978		$	5,474

Pre-opening expenses as a percentage of sales for the twelve and twenty-eight weeks ended April 10, 2011 were approximately 0.4% and 0.3%, respectively, compared to approximately 0.6% and 0.5%, respectively, for the same periods of the prior fiscal year.

Relocation, store closure and lease termination costs for the twelve and twenty-eight weeks ended April 10, 2011 were approximately $1.0 million and $4.1 million, respectively, compared to a credit of approximately $2.7 million and expense of approximately $9.7 million, respectively, for the same periods of the prior fiscal year. The Company recorded lease termination costs totaling approximately $1.2 million and $11.3 million during the twelve and twenty-eight weeks ended April 11, 2010, respectively, to increase reserves for closed properties due to the downturn in the real estate market and actual exit costs. These adjustments during the twelve weeks ended April 11, 2010 were offset by a gain of approximately $3.2 million from the sale of a non-operating property and a reduction of approximately $2.9 million in store closure reserve liabilities related to one store sold under the FTC settlement and one early lease termination.

The number of stores opened and relocated were as follows:

	Twelve weeks ended		Twenty-eight weeks ended
	April 10,	April 11,	April 10,	April 11,
	2011	2010	2011	2010
New stores	2	3	5	9
Relocated stores	1	—	1	—

Interest expense for the twelve and twenty-eight weeks ended April 10, 2011 decreased to approximately $1.3 million and $3.6 million, respectively, from approximately $7.8 million and $18.3 million, respectively, for the same periods of the prior fiscal year. The decrease in interest expense is due primarily to a lower average balance outstanding on the term loan and lower effective interest rates.

Investment and other income, which includes interest income, investment gains and losses, rental income and other income, totaled approximately $1.9 million and $4.6 million for the twelve and twenty-eight weeks ended April 10, 2011, respectively, compared to approximately $1.9 million and $3.7 million, respectively, for the same periods of the prior fiscal year. The increase in investment and other income during the twenty-eight weeks ended April 10, 2011 compared to the same period of the prior year is due principally to higher invested balances.

Income taxes for the twelve and twenty-eight weeks ended April 10, 2011 resulted in an effective tax rate of approximately 37.0% and 38.5%, respectively, compared to approximately 40.5% and 40.7%, respectively, for the same periods of the prior fiscal year. The decline in the effective tax rate is primarily due to certain tax savings initiatives and investments.

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Liquidity and Capital Resources and Changes in Financial Condition

The following table summarizes the Company’s cash and short-term investments as of the dates indicated (in thousands):

	April 10,		September 26,
	2011		2010
Cash and cash equivalents	$	162,103	$	131,996
Short-term investments — available-for-sale securities	391,846		329,738
Total	$	553,949	$	461,734

Additionally, the Company had restricted cash balances totaling approximately $86.8 million at April 10, 2011 and September 26, 2010 and long-term investments in available-for-sale securities totaling approximately $80.4 million and $96.1 million at April 10, 2011 and September 26, 2010, respectively.

We generated cash flows from operating activities totaling approximately $402.8 million during the twenty-eight weeks ended April 10, 2011 compared to approximately $343.0 million during the same period of the prior fiscal year. During the twenty-eight weeks ended April 10, 2011, increased cash flows from operating activities were primarily driven by increased net income.

Net cash used in investing activities totaled approximately $220.0 million for the twenty-eight weeks ended April 10, 2011 compared to approximately $587.1 million for the same period of the prior fiscal year. Our principal historical capital requirements have been the funding of the development or acquisition of new stores and acquisition of property and equipment for existing stores. The required cash investment for new stores varies depending on the size of the new store, geographic location, degree of work performed by the landlord and complexity of site development issues. Capital expenditures for the twenty-eight weeks ended April 10, 2011 totaled approximately $169.6 million, of which approximately $89.5 million was for new store development and approximately $80.1 million was for remodels and other additions. Capital expenditures for the twenty-eight weeks ended April 11, 2010 totaled approximately $147.0 million, of which approximately $111.0 million was for new store development and approximately $36.0 million was for remodels and other additions. As of May 4, 2011, the Company expected to open an additional ten stores and two major expansions in fiscal year 2011.

The following table provides information about the Company’s store development activities during fiscal year 2010 and fiscal year-to-date through May 4, 2011:

				Properties	Total
	Stores opened		Stores opened	tendered	leases signed
	during fiscal		during fiscal	as of	as of
	year 2010		year 2011	May 4, 2011	May 4, 2011(1)
Number of stores (including relocations)	16		7	20	61
Number of relocations	—		2	5	7
Number of lease acquisitions, ground leases and owned properties	—		—	4	4
New areas	4		—	1	12
Average store size (gross square feet)	42,600		40,900	37,900	36,600
Total square footage	682,200		286,400	757,400	2,249,100
Average tender period in months	10.9
Average pre-opening expense per store(2)	$	2.6 million
Average pre-opening rent per store	$	1.2 million
Average development cost per square foot	$	261

(1) Includes leases for properties tendered

(2) Includes rent

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The following table provides additional information about the Company’s estimated store openings for the remainder of fiscal year 2011 through 2014 based on the Company’s current development pipeline. We believe we will produce operating cash flows in excess of the capital expenditures needed to open the 61 stores in our store development pipeline. We believe the investments we are making in our new and existing stores will result in substantial earnings growth in the future. These openings reflect estimated tender dates which are subject to change and do not incorporate any potential new leases, terminations or square footage reductions:

			Average		Ending
			new store	Ending	square
	Total		square	square	footage
	openings	Relocations	footage	footage(1)	growth
Fiscal year 2011 remaining stores in development	10	4	36,500	11,786,200	5	%
Fiscal year 2012 stores in development	20	—	35,900	12,503,300	6	%
Fiscal year 2013 stores in development	22	3	36,300	13,228,900	6	%
Fiscal year 2014 stores in development	9	—	39,300	13,582,500	3	%
Total	61	7

(1) Reflects seven openings and one expansion year to date and two additional expansions in fiscal year 2011.

Net cash used in financing activities totaled approximately $155.2 million for the twenty-eight weeks ended April 10, 2011 compared to net cash provided by financing activities totaling approximately $27.6 million for the same period of the prior fiscal year.

The Company had outstanding a $700 million, five-year term loan agreement due in 2012. During the twenty-eight weeks ended April 10, 2011, the Company repaid $300 million on the term loan and at April 10, 2011 had $190 million outstanding under this agreement. Subsequent to the end of the second quarter of fiscal year 2011, the Company repaid the remaining $190 million on the term loan. The Company also has outstanding a $350 million revolving line of credit that extends to 2012. At April 10, 2011 and September 26, 2010 the Company had no amounts drawn under this agreement. The amount available to the Company under the agreement was effectively reduced to approximately $342.9 million by outstanding letters of credit totaling approximately $7.1 million at April 10, 2011 and September 26, 2010. The Company’s obligations under these facilities are secured by liens on certain of the Company’s assets, including stock of our subsidiaries. The term loan and revolving line of credit contain certain affirmative covenants including maintenance of certain financial ratios and certain negative covenants including limitations on additional indebtedness and payments as defined in the agreement. At April 10, 2011 we were in compliance with all applicable debt covenants.

Net proceeds to the Company from team members’ stock plans for the twenty-eight weeks ended April 10, 2011 totaled approximately $153.1 million compared to approximately $34.3 million for the same period of the prior fiscal year. The Company intends to keep its broad-based stock option program in place, but also intends to limit the number of shares granted in any one year so that annual earnings dilution from share-based payment expense will not exceed 10%. The Company believes this strategy is best aligned with its stakeholder philosophy because it limits future earnings dilution from options and at the same time retains the broad-based stock option plan, which the Company believes is important to team member morale, its unique corporate culture and its success. At April 10, 2011 and September 26, 2010, approximately 13.6 million shares and 12.7 million shares of our common stock were available for future stock incentive grants.

During the first quarter of fiscal year 2011, the Company’s Board of Directors reinstated a quarterly cash dividend to shareholders. Following is a summary of dividends declared per common share during fiscal year 2011 (in thousands, except per share amounts):

Date of	Dividend per		Date of	Date of	Total
declaration	common share		record	payment	amount
December 8, 2010	$	0.10	January 10, 2011	January 20, 2011	$	17,348
February 27, 2011	0.10		April 12, 2011	April 22, 2011	17,572		(1)

(1) Dividend accrued at April 10, 2011

The Company is committed under certain capital leases for rental of certain equipment, buildings and land. These leases expire or become subject to renewal clauses at various dates through 2054.

The effect of exchange rate changes on cash included in the Consolidated Statements of Cash Flows resulted in an increase in cash and cash equivalents totaling approximately $2.4 million for the twenty-eight weeks ended April 10, 2011 compared to

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approximately $1.6 million for the same period of the prior fiscal year. These changes principally reflect the relative strengthening of the Canadian dollar compared to the U.S. dollar during these periods.

Our principal historical sources of liquidity have been cash generated by operations, available cash and cash equivalents, short-term investments and amounts available under our revolving line of credit. Absent any significant change in market condition, we expect planned expansion and other anticipated working capital and capital expenditure requirements for the next twelve months will be funded by these sources. There can be no assurance, however, that the Company will continue to generate cash flows at or above current levels or that our revolving line of credit and other sources of capital will be available to us in the future.

Contractual Obligations

The following table shows payments due by period on contractual obligations as of April 10, 2011 (in thousands):

			Less than 1		1-3		3-5		More than 5
	Total		year		years		years		years
Long-term debt obligations	$	190,000	$	—	$	190,000	$	—	$	—
Estimated interest on long-term debt obligations	424		424		—		—		—
Capital lease obligations (including interest)	35,954		2,035		4,188		4,220		25,511
Operating lease obligations(1)	5,972,983		290,746		656,440		683,776		4,342,021
Total	$	6,199,361	$	293,205	$	850,628	$	687,996	$	4,367,532

(1) Amounts exclude taxes, insurance and other related expense

Gross unrecognized tax benefits and related interest and penalties at April 10, 2011 were approximately $14.9 million. These amounts have been excluded from the contractual obligations table because a reasonably reliable estimate of the period of cash settlement with the respective taxing authorities cannot be determined due to the high degree of uncertainty regarding the timing of future cash outflows associated with these liabilities.

We periodically make other commitments and become subject to other contractual obligations that we believe to be routine in nature and incidental to the operation of the business. Management believes that such routine commitments and contractual obligations do not have a material impact on our business, financial condition or results of operations.

Off-Balance Sheet Arrangements

Our off-balance sheet arrangements at April 10, 2011 consist of operating leases disclosed in the above contractual obligations table and outstanding letters of credit discussed in Note 6 to the consolidated financial statements, “Long-Term Debt.” We have no other off-balance sheet arrangements that have had, or are reasonably likely to have, a material current or future effect on our consolidated financial statements or financial condition.

Recent Accounting Pronouncements

Recent accounting pronouncements are included in Note 2 to the consolidated financial statements, “Recent Accounting Pronouncements.”

Item 4. Controls and Procedures

The Company maintains disclosure controls and procedures that are designed to ensure that information required to be disclosed by us in the reports we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms, and that such information is accumulated and communicated to our management, including our Co-Chief Executive Officers (principal executive officers) and Chief Financial Officer (principal financial officer), to allow timely decisions regarding required disclosure. The Company’s management, with the participation of the Company’s Co-Chief Executive Officers and Chief Financial Officer, has evaluated the effectiveness of the Company’s disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of the end of the period covered by this report. Based on such evaluation, the Company’s Co-Chief Executive Officers and Chief Financial Officer have concluded that, as of the end of such period, the Company’s disclosure controls and procedures were effective of the end of the period covered by this report.

There have been no changes in the Company’s internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during the most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting.

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Part II. Other Information

Item 1. Legal Proceedings

The Company is exposed to claims and litigation matters arising in the ordinary course of business and uses various methods to resolve these matters in a manner that we believe best serves the interests of our stakeholders. We have exposures to loss contingencies arising from pending or threatened litigation for which assessing and estimating the outcomes of these matters involve substantial uncertainties.

On October 27, 2008, Whole Foods Market was served with the complaint in Kottaras v. Whole Foods Market, Inc., a putative class action filed in the United States District Court for the District of Columbia, seeking treble damages, equitable, injunctive, and declaratory relief and alleging that the acquisition and merger between Whole Foods Market and Wild Oats violates various provisions of the federal antitrust laws. This case continues to be in the early stages of litigation. Whole Foods Market cannot at this time predict the likely outcome of this judicial proceeding or estimate the amount or range of loss or possible loss that may arise from it. The Company has not accrued any loss related to the outcome of this case as of April 10, 2011.

The Company evaluates contingencies on an ongoing basis and has established loss provisions for matters in which losses are probable and the amount of loss can be reasonably estimated. Legal settlement liabilities are included in the “Other current liabilities” line item on the Consolidated Balance Sheets. We believe the recorded reserves in our consolidated financial statements are adequate in light of the probable and estimable liabilities. However, resolution of contingencies resulting in amounts that vary materially from the Company’s current estimates could have a material adverse effect on the Company’s results of operations, cash flows, or financial condition.

Item 6. Exhibits

Exhibit	22.1	Submission of Matters to a Vote of Security Holders (1)
Exhibit	31.1	Certification of Co-Chief Executive Officer Pursuant to 17 CFR 240.13a — 14(a)
Exhibit	31.2	Certification of Co-Chief Executive Officer Pursuant to 17 CFR 240.13a — 14(a)
Exhibit	31.3	Certification of Chief Financial Officer Pursuant to 17 CFR 240.13a — 14(a)
Exhibit	32.1	Certification of Co-Chief Executive Officer Pursuant to 18 U.S.C. Section 1350
Exhibit	32.2	Certification of Co-Chief Executive Officer Pursuant to 18 U.S.C. Section 1350
Exhibit	32.3	Certification of Chief Financial Officer Pursuant to 18 U.S.C. Section 1350
Exhibit	101	The following financial information from the Company’s Quarterly Report on Form 10-Q, for the period ended April 10, 2011, formatted in eXtensible Business Reporting Language: (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations, (iii) Consolidated Statements of Shareholders’ Equity, (iv) Consolidated Statements of Cash Flows, (v) Notes to Consolidated Financial Statements (2)

(1)Filed as Item 5.07 in Registrant’s Form 8-K filed February 28, 2011 and incorporated herein by reference.

(2)Pursuant to Rule 406T of Regulation S-T, the Interactive Data Files hereto are deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933, as amended, are deemed not filed for purposes of Section 18 of the Securities and Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

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SIGNATURE

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

	WHOLE FOODS MARKET, INC.
Date: May 20, 2011	By:	/s/ Glenda Flanagan
	Glenda Flanagan
	Executive Vice President and Chief Financial Officer
	(Duly authorized officer and principal financial officer)

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EX-31.1

Exhibit 31.1

CERTIFICATIONS

I, John Mackey, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 20, 2011

/s/John Mackey

John Mackey

Co-Chief Executive Officer

EX-31.2

Exhibit 31.2

CERTIFICATIONS

I, Walter Robb, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 20, 2011

/s/Walter Robb

Walter Robb

Co-Chief Executive Officer

EX-31.3

Exhibit 31.3

CERTIFICATIONS

I, Glenda Flanagan, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 20, 2011

/s/Glenda Flanagan

Glenda Flanagan

Chief Financial Officer

EX-32.1

Exhibit 32.1

Certification by Co-Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report of Whole Foods Market, Inc. (the “Company”) on Form 10-Q for the period ending April 10, 2011 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, John Mackey, Co-Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/John Mackey

John Mackey

Co-Chief Executive Officer

May 20, 2011

EX-32.2

Exhibit 32.2

Certification by Co-Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report of Whole Foods Market, Inc. (the “Company”) on Form 10-Q for the period ending April 10, 2011 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Walter Robb, Co-Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/Walter Robb

Walter Robb

Co-Chief Executive Officer

May 20, 2011

EX-32.3

Exhibit 32.3

Certification by Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report of Whole Foods Market, Inc. (the “Company”) on Form 10-Q for the period ending April 10, 2011 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Glenda Flanagan, Chief Financial Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/Glenda Flanagan

Glenda Flanagan

Chief Financial Officer

May 20, 2011