WHOLE FOODS MARKETANNUAL 2013 REPORT

Selling the highest quality natural and organic products available. Our “bottom line” ultimately depends on our ability to satisfy all of our stakehold-ers. Our goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, communities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stakeholders.

Our core values reflect this sense of col-lective fate and are the soul of our company. Our core values define us as a company, and aspart of a movement to bring healthy food alternatives to the planet:. We educate them about natural and organic foods, health, nutrition and the environment. Our goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, communities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stakeholders. Our core values reflect this sense of collective fate and are the soul of our company.

it took just ideas to grow our business

3Satisfying and delighting our cus-tomers. They are our most important stakeholders in our business and the life-blood of our business. Only by satisfying our customers first do we have the opportunity to satisfy the needs of our other stakehold-ers. We go to extraordinary lengths to satisfy and delight our customers. We want to meet or exceed their expectations on every shopping trip. We know that by doing so we turn customers into advocates for our business. Advocates do more than shop with us, they talk about Whole Foods to their friends and others in all locations.

We want to serve our customers com-petently, efficiently, and with flair. Only by satisfying our customers first do we have the opportunity to satisfy the needs of our other stakeholders. We go to extraordi-nary lengths forour customers. We want to meet or exceed their expectations on every shopping trip. We want to serve our customers with flair. Only by satisfying our customers first do we have the opportunity to satisfy our other stakeholders.

Caring about our communities and our environment. We support organic farmers, growers and the environ-ment through our commitment to sus-tainable agriculture and by expanding the market for organic products. We respect our environment and recycle, reuse, and reduce our waste wherever and whenever we can. We recognize our responsibility to be active participants in our local communities.

We give a minimum of 5% of our profits every year to a wide variety of com-munity and non-profit organizations. Our trade partners are our allies in serving our stakeholders. We treat them with respect, fairness and integrity at all times and expect the same in return. We respect our environ-ment and recycle, reuse, and reduce our waste wherever and whenever we can. We recognize our responsibility to be active participants in our local communities. Our trade partners are our allies in serving our stakeholders. We treat them with respect, fairness and integrity at all times and expect the same in return from everyone.

Einstein’s Three Rules of Work 1. Out of clutter find simplicity 2. From discord find harmony 3. In the middle of difficulty lies opportunity— ALBERT EINSTEIN

shareholders’ letterDear Fellow Stakeholders:

This was the best year in our company’s 32-year history. We delivered our strongest financial performance, breaking records on many levels. Our sales approached $12 billion, translating to sales per gross square foot of $932. We opened 25 new stores, expanding into eight new markets, and increased our ending square footage 8% to 12.7 million. We reported our eleventh consecutive quarter of comparable store sales growth of 7.8% or better, improved operating margin 94 basis points to 6.4%, generated over $1 billion in EBITDA, and grew diluted earnings per share by 31% to $2.52. Our stellar results substantially exceeded our own expectations, as well as Wall Street’s, driving our stock price to a new all-time high of $101.86 and resulting in a 31% increase for the calendar year versus the 13% increase for the S&P 500 Index.

Our solid execution, capital discipline, and increasing stock price generated $1.3 billion of cash during the fiscal year through a com-bination of $920 million in cash flow from operations and $370 million in proceeds from team member stock option exercises. We invested $456 million in new and exist-ing stores, returned $95 million in quarterly dividends to our shareholders, and repur-

chased $29 million of common stock. Our total cash and investments nearly doubled over the prior year, increasing $745 million to $1.5 billion. Our strong operating trends and improved credit metrics resulted in two corporate rating upgrades from Standard & Poor’s, and we are rated investment grade once again.

With confidence that we are well posi-tioned to maintain a healthy cash reserve and internally fund our accelerated new store growth, subsequent to the fiscal year end, our Board of Directors increased our quarterly dividend by 43% to $0.20 per share, granted an additional $300 million in stock repurchase authority, and declared a special dividend of $2 per share.

We are proud that we continue to gain market share from our competitors and attribute much of our success to our visible value efforts which have positively impacted our price image. In 2012, we appropriately navigated the balance between price invest-ments, gross margin and sales momentum. We posted robust sales gains, better-than-historical gross margin results, and decreased the pricing gap versus our competitors on known value items to its narrowest margin ever recorded in our history.

Our stellar results substantially exceeded our own expectations, as well as Wall Street’s, driving our stock price to a new all-time high of $101.86 and resulting in a 31% increase for the calendar year versus the 13% increase for the S&P 500 Index.

Our solid execution, capital discipline, and increasing stock price generated $1.3 billion of cash during the fiscal year through a com-bination of $920 million in cash flow from operations and $370 million in proceeds from team member stock option exercises.

John Mackey, Chairman and CEO

Approximately 17% of our existing square footage was acquired, and while we may continue to pursue acquisitions of smaller chains that provide access to desirable geo-graphic areas and experienced team mem-bers, such acquisitions are not expected to significantly impact our future store growth or financial results. Our growth strategy is to expand primarily through new store openings. We have a disciplined, opportu-nistic real estate strategy, opening stores in existing trade areas as well as new areas, including international locations. We typi-cally target stores located on premium real estate sites, and while we may open stores as small as 15,000 square feet or as large as 75,000 square feet, the majority of our new stores are expected to fall in the range of 35,000 to 45,000 square feet going forward.As of September 30, 2012, we operated 335 stores: 322 stores in 39 U.S. states and the District of Columbia; 7 stores in Canada; and 6 stores in the United Kingdom. We own 12 stores, two distribution facilities and land for one store in development, including the adjacent property. We also own a build-ing and land, which is leased to third parties. We have a disciplined, opportunistic real estate strategy,.

Annual Revenue

2009 2010 2011 2012 2013

$6.2$5.9 $6.5 $7.0 $7.5

Financial Highlights

ANNUAL REVENUE (IN MILLIONS)

Consolidated Balance SheetSept. 30, 2012 Sept.28, 2011 Sept. 29, 2010 Sept. 30, 2009 Sept. 26, 2008

Sales $11,698,828 10,107,787 9,005,794 8,031,620 7,953,912Cost of goods sold 7,543,054 6,571,238 5,869,519 5,276,493 5,246,468Gross profit 4,155,774 3,536,549 3,136,275 2,755,127 2,707,444Direct store expenses 2,983,419 2,628,811 2,376,590 2,146,626 2,108,679

General expenses 372,065 310,920 272,449 243,749 270,428Pre-openening expenses 46,899 40,852 38,044 49,218 55,554Relocation, store closure and lease termination costs 9,885 8,346 11,217 31,185 36,545Operating income 743,506 547,620 437,975 284,349 236,238Interest expense (354) (3,882) (33,048) (36,856) (36,416)Investment and other income 8,892 7,974 6,854 3,449 6,697Income before income taxes 752,044 551,712 411,781 250,942 206,519Provision for income taxes 286,471 209,100 165,948 104,138 91,995Net income 465,573 342,612 245,833 146,804 114,524Basic earnings per share 2.55 1.96 1.45 0.85 0.82Weighted average shares outstanding 182,401 175,221 166,244 140,414 139,886Diluted earnings per share 2.52 1.93 1.43 0.85 0.82Weighted average shares outstanding, diluted basis 184,444 177,279 171,710 140,414 140,011Dividends declared per common share 0.56 0.40 — — 0.60Consolidated Balance Sheets Data

Net working capital 1,125,443 573,783 413,647 371,356 (43,571)Total assets 5,294,216 4,292,075 3,986,540 3,783,388 3,380,736Long-term debt (including current maturities) 24,122 17,905 508,698 739,237 929,170Shareholders’ equity 3,802,469 2,991,305 2,373,258 1,627,876 1,506,024

2009 2010 2011 2012 2013

2009 2010 2011 2012 2013

GROWTH REPORT (IN MILLIONS)

EXPENSE REPORT (IN THOUSANDS)

Expense and Growth Reports

$5.7 $6.2 $6.4 $6.4 $6.6

$422 $418 $430 $425 $415

We have signed 45 new leases over the last 12 months and, based on our performing. We opened a record number of new stores in 2012 and expect this to continue into 2013 and 2014.

When the first Whole Foods Market opened in September 1980, we had no idea that we would become the 8th cur-rent development pipeline, are on track to accelerate our store openings and ending square footage growth as well. For the last six quarters, on average our new store class consisted of 22 stores open for approxi-mately largest public food and drug retailer in the U.S., ranking #264 on the Fortune 500, with over 340 stores in the through 2014. six months. At 38,000 square feet in size, they produced average weekly sales of $564,000 translating to sales U.S., Canada, and the U.K. per square foot of $777, and generated a contribution margin of approxi-mately 6%. These outstanding results,

We are committed to growing at a culturally sustainable rate and believe 1,000 stores in the U.S. is an achievable People are increasingly embracing healthier lifestyles to improve the quality of their lives and minimize Our outlook for fiscal year 2013

reflects another year of healthy comparable store sales growth and incremental Ulti-mately depends on our ability to satisfy all of our stakeholders. Our goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, com-munities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stake-holders. Our core values reflect this sense of collective fate and are the soul of Whole Foods, Inc.

2013

U.S. STOCKS31%

U.S. BONDS21%

INTERNATIONAL HOLDINGS

12%EMERGING EQUITIES31%

DOMESTIC EQUITIES

33%

Allocated Asset ChartApproximately 17% of our existing square footage was acquired, and while we may continue to pursue acquisitions of smaller chains that provide access to desirable geo-graphic areas and experienced team mem-bers, such acquisitions are not expected to significantly impact our future store growth or financial results. Our growth strategy is to expand primarily through new store openings. We have a disciplined, opportu-nistic real estate strategy, opening stores in existing trade areas as well as new areas, including international locations. We typi-cally target stores located on premium real estate sites, and while we may open stores as small as 15,000 square feet or as large as 75,000 square feet, the majority of our new stores are expected to fall in the range of 35,000 to 45,000 square feet going forward.

As of September 30, 2012, we operated 335 stores: 322 stores in 39 U.S. states and the District of Columbia; 7 stores in Canada; and 6 stores in the United Kingdom. We own 12 stores, two distribution facilities and land for one store in development, including the adjacent property. We also own a building and land, which is leased to third parties; a building on leased land, which we own.

Creating an atmosphere of friend-liness, creativity and growth. Our “bottom line” ultimately depends on an abil-ity to satisfy all of our stakeholders. The goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, communities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stakeholders. Our core values reflect this sense of collective fate and are the soul of our company. Our core values define us as a company, and aspart of a movement to bring healthy food alternatives to the planet:. We educate them about natural and organic foods, health, nutrition and the environ-ment. Our goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, communities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stakeholders. Our core values reflect this sense of collective fate of our company.

Educating the world about healthy choices.They are our most important stakeholders in our business and the life-blood of our business. Only by satisfying our customers first do we have the opportunity to satisfy the needs of our other stakeholders. We go to extraordinary lengths to satisfy and delight our customers. We want to meet or exceed their expectations on every shopping trip. We know that by doing so we turn customers into advocates for our busi-ness. Advocates do more than shop with us, they talk about Whole Foods to their friends and others. We want to serve our custom-ers competently, efficiently, and with flair. Only by satisfying our customers first do we have the opportunity to satisfy the needs of our other stakeholders. We go to extraordinary lengths forour customers. We want to meet or exceed their expec-tations on every shopping trip. We want to serve our customers with flair. Only by satisfying our customers first do we have the opportunity to satisfy everyone.

Valuing our partners in farming and produce. We support organic farm-ers, growers and the environment through our commitment to sustainable agriculture and by expanding the market for organic products. We respect our environment and recycle, reuse, and reduce our waste wher-ever and whenever we can. We recognize our responsibility to be active participants in our local communities. We give a minimum of 5% of our profits every year to a wide variety of community and non-profit orga-nizations. Our trade partners are our allies in serving our stakeholders. We treat them with respect, fairness and integrity at all times and expect the same in return. We respect our environment and recycle, reuse, and re-duce our waste wherever and whenever we can. We recognize our responsibility to stay active participants in our local communities. Our trade partners are our allies in serv-ing our stakeholders. We treat them with respect, fairness and integrity at all times and expect the same in return.

how we adhere to our basic core values

3

Three passions, simple but overwhelmingly strong, have governed my life: 1. the longing for love 2. the search for knowledge 3. and unbearable pity for the suffering of mankind.— BERTRAND RUSSELL

We focus on our ability to satisfy all of our stakeholders. Our goal is to balance the needs and desires of our customers, team members, shareholders, suppliers, com-munities and the environment while creating value for all. By growing the collective pie, we create larger slices for all of our stakeholders. Our core values reflect this sense of collective fate and are the soul of our company. Our solid execution, capital discipline, and increasing stock price gener-ated $1.3 billion of cash during the fiscal year through a combination of $920 million in cash flow from operations and $370 million in proceeds from team member stock option exercises. We invested $456 million in new and existing stores, returned $95 million in quarterly dividends to our shareholders, and repurchased $29 million of common stock. Our total cash and investments nearly doubled over the prior year, increasing $745 million to $1.5 billion. Our strong operating trends and improved credit metrics resulted in two corporate rating upgrades from Standard & Poor’s, and we are rated investment grade once again. Our core vaules are what make us a unique company, in every regard.

Our core values define us as a company, and aspart of a movement to bring healthy food alternatives to the planet:

• Selling the highest quality natural and organic products available

• Satisfying and delighting our customers

• Supporting team member happiness and excellence in service

• Creating wealth through profits, growth and prosperity

• Caring about our communities and our fragile environment

We are proud that we continue to gain market share from our competitors and attribute much of our success to our visible value efforts which have positively impacted our price image. In 2012, we appropriately navigated the balance between price invest-ments, gross margin and sales momentum. We posted robust sales gains, better-than-historical gross margin results, and decreased the pricing gap versus our competitors on known value items to its narrowest margin ever recorded in our history.

to us, growth just comes naturally.

550 Bowie Street, Austin, Texas 78703 703.567.3000

www.wholefoodsmarket.com