Certain statements in this Report on Form 10-K for the fiscal year ended September 28, 2014 (the “Original Form 10-K”). This Amendment No. 1 (the “Amendment”) amends Part III, Items 10 through 14 of the Original Form 10-Kand from time to include information previously omitted from the Original Form 10-Ktime in reliance on General Instruction G(3) to Form 10-K. General Instruction G(3) to Form 10-K provides that registrants may incorporate by reference certain information from a definitive proxy statement which involves the election of directors if such definitive proxy statement is filed with the Securities and Exchange Commission within 120 days after the end of the fiscal year. The Company does not anticipate that its definitive proxy statement involving the election of directors will be filed before January 26, 2015 (i.e., within 120 days after the end of the Company’s 2014 fiscal year). Accordingly, Part III of the Original Form 10-K is hereby amended and restated as set forth below. The information included herein as required by Part III, Items 10 through 14 of Form 10-K is more limited than what is required to be included in the definitive proxy statement to be filed in connection with our annual meeting of stockholders. Accordingly, the definitive proxy statement to be filed at a later date will include additional information related to the topics herein and additional information not required by Part III, Items 10 through 14 of Form 10-K.

This information should be read in conjunction with the consolidated financial statements and the NASDAQ Listing Rules.accompanying notes included in this report.

Whole Foods Market is the leading natural and organic foods supermarket, the first national “Certified Organic” grocer, and uniquely positioned as America’s Healthiest Grocery Store™. The Company incorporated in November 20111978, opened the first Whole Foods Market store in 1980, and December 2005. Mr. Sorenson’s holdings were correctedis based in footnotesAustin, Texas. We completed our initial public offering in January 1992, and our common stock trades on a Form 4 filed on June 6, 2014.

Compensation DiscussionWhole Foods Market is a mission-driven company that aims to set the standards of excellence in food retailing. Our motto – Whole Foods, Whole People, Whole Planet – emphasizes that our vision reaches far beyond food retailing. Our success is measured by customer satisfaction, team member happiness and Analysisexcellence, return on invested capital, active environmental stewardship, service in our local and global communities, and win-win supplier partnerships, among other things. 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 over the last 38 years.

The following section explains our compensation programs, with an emphasis on the compensationis a summary of our seven executive officers, who we referannual percentage sales and net long-lived assets by geographic area for the fiscal years indicated:

John MackeyA five-year summary of certain financial and Walter Robb, our Co-Chief Executive Officers

We believe that much of our principal executive officers (John Mackey and Walter Robb),success to date is because we remain a uniquely mission-driven company. The purpose of our principal financial officer (Glenda Flanagan) and the three most highly compensated executive officers other than the principal executive officers and principal financial officer. We have included an additional executive officer in orderbusiness is not only to present compensation informationgenerate profits but to create value for all of our executive officers.major stakeholders, each of which is linked interdependently. Our Core Values succinctly express this purpose:

We continually evaluatebelieve our compensation practices to ensure that they helphigh quality standards differentiate our stores from other supermarkets and enable us to achieve our compensation goals and align with our core values. Set forth below are some examples of practices currently in place that demonstrate our commitment to our goals and values.

We offer the long term qualifiedbroadest selection of high-quality natural and energetic team members who are enthusiastic about our mission and culture, providing themorganic products, with sufficient incomea strong emphasis on perishable foods. Our stores also feature a wide variety of non-GMO, vegan, gluten-free, dairy-free and other benefits to keep them focused on the Company as their employer. A further objectivespecial diet foods. An average store carries approximately 35,000 SKUs, with certain of our compensation programs islarger stores carrying up to reward each of our team members for their contribution to the Company. Finally, we endeavor to ensure that our compensation programs are perceived as fundamentally fair to all stakeholders.

The following five quantitative bonus criteria were selected at the beginningis a summary of annual percentage sales by product category for the fiscal year by the Compensation Committee in its discretion:years indicated:

Whole Foods Market is certified by California Certified Organic Farmers (“CCOF”), an independent, USDA-accredited, third-party certifier. CCOF’s Organic Certification Program for retailers verifies we handle organic goods according to stringent USDA guidelines. The list of 2014 criteria is different from the list of possible and actual criteria for 2013 in several respects:CCOF audit process confirms that we:

We offer more than 30,000 unique organic SKUs company-wide, covering all areas of our store including produce, packaged goods, bulk, frozen, dairy, meat, bakery, prepared foods, coffee, tea, beer, wine, cheese, nutritional supplements, vitamins, body care, pet foods, and household goods. More than 30% of our sales, outside of prepared foods and bakery, were organic in fiscal year 2016.

We announced our GMO (“genetically modified organism”) Transparency Initiative in 2013 and are well on our way to providing GMO transparency for the Compensation Committee selected six criteriafood we sell by September 1, 2018. Currently, we offer more than 30,000 certified organic items (which must be non-GMO to meet USDA organic standards) and more than 13,500 “Non-GMO Project Verified” products in our stores.

We strive to transform food shopping from a listchore into a dynamic experience by designing and operating stores with a lively, inspirational atmosphere, mission-oriented décor and well-trained team members. We offer an exciting product mix that emphasizes our high quality standards and healthy eating, with a range of thirteen possible criteria. For fiscal year 2014,choices at every price level, ever-changing selections, samples, open kitchens, scratch bakeries, hand-stacked produce, bulk departments and extensive prepared foods stations featuring wood-burning pizza ovens; burrito stations and ethnic foods; juicing and handcrafted coffee stations; and greens, beans and grains cooking bars, among others. To meet our customers’ evolving needs and preferences, we carefully evaluate and balance the Compensation Committee eliminated eight possibleblend between full- and self-service options. We also incorporate environmentally sustainable aspects into our store design, and many stores have bicycle racks and electric vehicle charging stations. Our stores typically include sit-down eating areas and customer service booths, and many stores offer special services such as personal shopping, online ordering, and home delivery through customer service or Instacart. Many of our urban stores offer sit-down wine bars and tap rooms featuring local and/or craft beer and wine, creating a destination for customer gathering. We believe our stores play a unique role as a third place, besides the home and office, where people can gather, interact and learn while at the same time discovering the many joys of eating and sharing food.

In selecting store locations, we use an internally developed model to analyze potential sites based on various criteria that had been includedsuch as education levels, interest in and awareness of natural and organic foods, population density and other demographic information within certain drive times. After we have selected a target site, our development group does a comprehensive site study and sales projection and works with our regional teams to develop construction and operating cost estimates. Each project must meet an internal Economic Value Added (“EVA®”) hurdle return, which for new stores generally is expected to be cumulative positive EVA in five years or less. In its simplest definition, EVA is equivalent to net operating profits after taxes minus a charge on the Bonus Plan since it was approved in 2009, sevencost of which had never been used.invested capital necessary to generate those profits. The reason for this elimination is that the Compensation Committee believed that the criteria it selected for fiscal year 2014 were the most useful measuresCompany’s calculated weighted average cost of performance, and it did not believe that the eight eliminated criteria were necessary at that time.

The required cash investment for new stores varies depending on the size of the store, geographic location, degree of landlord incentives and complexity of site development issues. To a significant degree, it also depends on how the project is structured,

including costs for elements that often increase or decrease rent, e.g., lease acquisition costs, shell and/or garage costs, and landlord allowances. Because of these differences, the average development cost per square foot may vary significantly from project to project, and therefore, the Compensation Committee did not believe that year-over-year improvement in this metric was necessarily the desired result or the right goal for executive officers. The Compensation Committee believes that the ROIC metric used forproject.

In fiscal year 2014 better reflects appropriate levels2016, we launched a value store format, 365 by Whole Foods Market. As a second growth vehicle, 365 complements the Whole Foods Market brand, allowing us to address the value-quality proposition through a convenient, smaller footprint and curated product selection. Our 365 stores feature a streamlined operating model, centralized buying, and inventory auto-replenishment. We are using our many learnings from our first three 365 openings to shape and evolve not only future 365 stores but Whole Foods Market stores as well.

The Company’s average weekly sales and gross profit as a percentage of capital investmentsales are typically highest in new stores.

All of our full-time and part-time team members are eligible to receive stock options through annual leadership grants or through service hourservice-hour grants once they have accumulated 6,000 service hours (approximately three years of full-time employment). We believe that stock options are a beneficial compensation tool because they link our team members’ interests with those of our shareholders, they are well suited to broad-based grants, they are easy to understand, and team members can control the timing of their taxable event. Approximately 94% of the equity awards granted under ourthe Company’s stock plan since its inception in 1992 have been granted to team members who are not executive officers. Each

We promote the health of our executive officers (other than Mr. Mackey, who has voluntarily electedteam members through two voluntary programs. The Total Health Immersion Program provides educational opportunities for team members that are paid by the Company. The Healthy Discount Incentive Program offers additional store discounts of up to 35%, going beyond the standard store discount that all team members receive, based on meeting designated biometric criteria for cholesterol/LDL, BMI or waist-height ratio, blood pressure, and being nicotine-free.

Food retailing is a large, intensely competitive industry. Our competition includes but is not limited to receive stock option grants) receives stock optionlocal, regional, national and international conventional and specialty supermarkets, natural foods stores, warehouse membership clubs, online retailers, smaller specialty stores, farmers’ markets, restaurants, and home delivery and meal solution companies, each of which competes with us on the basis of store ambiance and experience, product selection and quality, customer service, price, convenience or a combination of these factors.

Created in 2005, Whole Planet Foundation (www.wholeplanetfoundation.org) is an independent, nonprofit organization whose mission is to empower the poor through microcredit, with a focus on developing-world communities that supply our stores with product. Program grants are funded in part by the sale of products under the Company’s stock incentive plan. Service hourWhole Trade Guarantee Program, along with support from customers, suppliers and team members. As of June 30, 2016, Whole Planet Foundation has partnered with 83 unique microfinance institutions to facilitate more than $70 million in various donor-funded grants for 143 projects in 69 countries where the Company sources products. Over 1.5 million borrower families (88% women) have received loans, which are allocatedbeing used for home-based businesses.

Whole Kids Foundation (www.wholekidsfoundation.org), an independent nonprofit organization founded in 2011, is dedicated to improving children’s nutrition by supporting schools and inspiring families. The foundation provides grants for school gardens and salad bars and offers cooking and nutrition education for teachers and staff. Through the generosity of Whole Foods Market customers, suppliers and community donors, approximately 3,650 schools in the U.S. and Canada have received school garden grants, and over 70 have received honey bee hive grants. In addition, Whole Foods Market and Whole Kids Foundation, in partnership with Let’s Move Salad Bars to Schools, have provided approximately 4,700 salad bars to schools around the country, and more than 11,000 teachers and staff have received nutrition inspiration.

The following table sets forth the name, age, and position of each eligibleof the persons who was serving as an executive officer of the Company as of November 11, 2016:

The Company uses 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 team member (includinghealth care benefits. Liabilities associated with the risks that are retained by the Company are estimated, in part, by considering historical claims experience, demographic factors, severity factors and other actuarial assumptions. In addition, a significant number of our executive officers)stores are in locations that could be affected by natural disasters. In the event of a natural disaster, the Company could incur significant losses and significant expenditures in order to resume operations. Our results could be materially impacted by claims and other expenses related to such plans if future occurrences and claims differ from these assumptions and historical trends.

We believe our Company has built an excellent reputation as a food retailer, socially responsible corporation and employer, and we believe our continued success depends on our ability to preserve, grow and leverage the value of our brand. Brand value is based in large part on the proportionperceptions of subjective qualities, and even isolated incidents can erode trust and confidence, particularly if they result in adverse publicity, governmental investigations or litigation, which can negatively impact these perceptions and our business. We believe that many customers choose to shop our stores because of their total accumulated service hours. With respectinterest in health, nutrition and food safety and that they hold us to annual leadership grants,a higher food safety standard than other supermarkets. There is increasing governmental scrutiny of and public awareness regarding food safety. The real or perceived sale of contaminated food products by us could result in government enforcement action, private litigation, product recalls and other liabilities, the settlement or outcome of which might have a material adverse effect on our Compensation Committee providesoperating results and brand value.

We source our products from a discretionary awardvariety of local, regional, national and international suppliers, and we rely on them to meet our quality standards and supply products in a similar numbertimely and efficient manner. There is, however, no assurance that quality natural and organic products will be available to meet our needs. Competition has increased for natural, organic, sustainably-sourced, and responsibly-grown products. As other competitors significantly increase their natural and organic product offerings, if new laws require the reformulation of optionscertain products to each executive officer. meet tougher standards, or if natural disasters or other catastrophic events occur, the supply of these products may be constrained.

From time to time, we are party to legal proceedings, including matters involving personnel and employment issues, personal injury, product liability, protecting our Compensation Committeeintellectual property, acquisitions, and other proceedings arising in the ordinary course of business. Additionally, we are occasionally subject to industry-wide or class-action claims arising from the products we carry or industry-specific business practices. Further, we are involved in several securities class action litigation matters. Additional volatility in the price of our securities could result in additional securities class action litigation matters. Our results could be materially impacted by the decisions and expenses related to pending or future proceedings.

During fiscal year 2016, we entered into a $500 million revolving line of credit that extends to 2020, and we completed an offering of $1.0 billion aggregate principal amount of 5.2% senior notes due 2025. Changes in our credit ratings, or in the interest rate environment, could have an adverse impact on our financing costs. A significant portion of our future cash flow from operating activities may be dedicated to the repayment of our indebtedness. Our indebtedness could limit our ability to obtain additional financing for working capital, capital expenditures, debt service requirements, acquisitions or other purposes in the future. There is no guarantee that we will be able to meet our debt service obligations. If we fail to comply with our debt covenants, we will be in default, in which case there can be no assurance that we would be able to cure the default, receive waivers from our lenders, amend the loan agreement or refinance the debt. See Note 9 of the Notes to Consolidated Financial Statements in Part II, “Item 8. Financial Statements and Supplementary Data,” of this report.

We cannot predict the nature of future laws, regulations, interpretations or applications, or determine what effect either additional government regulations or administrative orders, when and if promulgated, or disparate local, state, federal and international regulatory schemes would have on our business in the future. They could, however, require the reformulation of certain products to meet new standards, the recall or discontinuance of certain products not able to be reformulated, additional recordkeeping, expanded documentation of the properties of certain products, expanded or different labeling and/or scientific substantiation. Any or all of such requirements could have an adverse effect on our operating results.

The Company’s management is responsible for establishing and maintaining adequate internal control over financial reporting. An internal control system, no matter how well designed and operated, can provide only reasonable, not absolute, assurance that additional equity grants, including possible restricted share issuances,the objectives of the control system are warrantedmet. Further, the design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Because of the inherent limitations in orderall internal control systems, internal control over financial reporting could limit our ability to reward exceptional performance, motivate future strong performance, retain valuable team membersreport our financial results accurately and keeptimely or to detect and prevent fraud, and could expose us to litigation or adversely affect the Company competitive.market price of our common stock. The Company’s management concluded that its internal control over financial reporting was effective as of September 25, 2016. See Management’s Report on Internal Control over Financial Reporting in Part 11, “Item 9A. Controls and Procedures,” of this report.

Our Compensation Committeecontinued growth depends on our ability to increase sales in our comparable stores and open new stores. Our growth strategy includes opening new stores in existing and new areas and operating those stores successfully. The Company’s average weekly sales and gross profit as a percentage of sales are typically highest in the second and third fiscal quarters, and lowest in the fourth fiscal quarter due to seasonally slower sales during the summer months. Gross profit as a percentage of sales is also lower in the first fiscal quarter due to the product mix of holiday sales.

Under the share repurchase programs, purchases can be made from time to time using a variety of methods, which may include open market purchases. The specific timing, price and size of purchases will depend on prevailing stock prices, general economic and market conditions, and other considerations. Purchases may be made through a Rule 10b5-1 plan pursuant to pre-determined metrics set forth in such plan. The Board’s authorization of the share repurchase program does not haveobligate the Company to acquire any particular amount of common stock, and the program may be suspended or discontinued at any time.

During the first quarter of fiscal year 2016, the Board authorized an exact formula for allocating between cashincrease in the Company’s quarterly dividend to $0.135 per common share from $0.13 per common share. The following table provides a summary of dividends declared per common share during fiscal years 2016 and non-cash compensation, and its allocation may change2015 (in millions, except per share amounts):

On November 2, 2016, the Board authorized an increase in the Company’s quarterly dividend to $0.14 per common share from year to year. In determining$0.135 per common share. The Company will pay future dividends at the discretion of the Board. The continuation of these payments, the amount of such awards, our Compensation Committee considersdividends, and the form in which dividends are paid (cash or stock) depend on many factors, including the results of operations and the financial condition of the Company. Subject to these qualifications, the Company currently expects to pay dividends on a quarterly basis.

Our off-balance sheet arrangements at September 25, 2016 consisted of operating leases disclosed in the above contractual obligations table, as well as the Credit Agreement discussed above. Additionally, we enter into forward purchase agreements for certain exceptions,products in the ordinary course of business. Purchase commitments do not exceed anticipated use within an operating cycle. 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.

The preparation of our financial statements in conformity with generally accepted accounting principles requires us to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, expenses and related disclosures of contingent assets and liabilities. Actual amounts may differ from these estimates. We base our estimates on historical experience and on various other assumptions and factors that we schedule equitybelieve to be reasonable under the circumstances. On an ongoing basis, we evaluate the continued appropriateness of our accounting policies and resulting estimates to make adjustments we consider appropriate under the facts and circumstances.

The Company maintains several share-based incentive plans. We grant dates well in advanceboth options to purchase common stock and restricted common stock under our Whole Foods Market 2009 Stock Incentive Plan. Options outstanding are governed by the original terms and conditions of any actual grant.the grants, unless modified by a subsequent agreement. Options are granted at an option price equal to the market value of the stock at the grant date and generally vest ratably over a four- or nine-year period beginning one year from grant date and have a five, seven or ten year term. The grant date is established when our Compensation Committeeonce the Company’s Board of Directors approves the grant and all key terms have been determined. Stock option grant terms and conditions are communicated to team members within a relatively short period of time. Our Company generally approves one primary stock option grant annually, occurring during a trading window. Restricted common stock is granted at the market price of the stock on the day of grant and generally vests over a four- or six-year period.