<PAGE>
 
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C.  20549

                                   FORM 10-Q
                                        


(X) QUARTERLY REPORT PURSUANT TO SECTION 13 OR SECTION 15(D) OF THE SECURITIES
     EXCHANGE ACT  OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 26, 1998

                                       OR


(_) TRANSITION REPORT PURSUANT TO SECTION 13 OR SECTION 15(D) OF THE SECURITIES
 EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM __________ TO _________.

Commission file number 0-21577


                            WILD OATS MARKETS, INC.
             (Exact name of registrant as specified in its charter)

      DELAWARE                                                  84-1100630
(State or other jurisdiction of                         (I.R.S. Employer Number)
Identification incorporation or 
organization)                    

                               3375 MITCHELL LANE
                          BOULDER, COLORADO 80301-2244
          (Address of principal executive offices, including zip code)

                                 (303) 440-5220
              (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  (_)

As of November 4, 1998, there were 13,066,342 shares outstanding of the
Registrant's Common Stock (par value $0.001 per share).
<PAGE>
 
                               TABLE OF CONTENTS
<TABLE> 
<CAPTION> 

                                                                                    PAGE

PART I.     FINANCIAL INFORMATION
<S>        <C>                                                                       <C>
Item 1.    Financial Statements

 
           Consolidated Balance Sheet
              September 26, 1998 (Unaudited) and December 27, 1997                    3
 
           Consolidated Statement of Operations (Unaudited)
              Three and Nine Months Ended September 26, 1998 and September 27, 1997   4
 
           Consolidated Statement of Cash Flows (Unaudited)
              Nine Months Ended September 26, 1998 and September 27, 1997             5
 
           Notes to Consolidated Financial Statements (Unaudited)                     6
 
Item 2.    Management's Discussion and Analysis of
              Financial Condition and Results of Operations                           7
 
Item 3.    Quantitative and Qualitative Disclosures
              About Market Risk                                                      12
 
PART II.   OTHER INFORMATION
 
Item 1.    Legal Proceedings                                                         13
Item 2.    Changes in Securities                                                     13
Item 3.    Defaults Upon Senior Securities                                           13
Item 4.    Submission of Matters to a Vote of Security Holders                       13
Item 5.    Other Information                                                         13
Item 6.    Exhibits and Reports on Form 8-K                                          13
 
SIGNATURES                                                                           14
 
</TABLE>

                                       2
<PAGE>
 
PART I.  FINANCIAL INFORMATION

ITEM 1.  FINANCIAL STATEMENTS
 
                            WILD OATS MARKETS, INC.
                           Consolidated Balance Sheet
                       (IN THOUSANDS, EXCEPT SHARE DATA)
<TABLE>
<CAPTION>
 
                                                 SEPTEMBER 26,   DECEMBER 27,
                                                      1998           1997
                                                  (Unaudited)
<S>                                              <C>             <C>
Assets
Current assets:
  Cash and cash equivalents                           $ 24,110       $ 46,686
  Accounts receivable (less allowance
     for doubtful accounts of $167 and
     $214, respectively)                                 1,324            674
  Inventories                                           25,125         21,539
  Income tax receivable                                    281            317
  Prepaid expenses and other current assets              1,499            735
  Deferred income taxes                                    984          1,447
                                                      --------       --------
     Total current assets                               53,323         71,398
                                                      --------       --------
Property and equipment, net                             88,334         56,285
Intangible assets, net                                  51,556         44,389
Deposits and other assets                                  938            841
Deferred income taxes                                      339            154
                                                      --------       --------
                                                      $194,490       $173,067
                                                      ========       ========
 
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                    $ 27,719       $ 22,487
  Accrued liabilities                                   16,700         11,848
                                                      --------       --------
     Total current liabilities                          44,419         34,335
Long-term debt                                                            467
Deferred income taxes                                    1,158          2,341
Other liabilities                                        2,065            801
                                                      --------       --------
                                                        47,642         37,944
                                                      --------       --------
 
Stockholders' equity:
  Preferred stock, $.001 par value; 5,000,000
     shares authorized; no shares
     issued and outstanding
  Common stock, $.001 par value; 20,000,000
     shares authorized; 13,046,512 and
     12,745,971 shares issued and outstanding               13             13
  Additional paid-in capital                           140,128        136,815
  Retained earnings (accumulated deficit)                6,922         (1,574)
  Accumulated other comprehensive income                  (215)          (131)
                                                      --------       --------
     Total stockholders' equity                        146,848        135,123
                                                      --------       --------
                                                      $194,490       $173,067
                                                      ========       ========
</TABLE>
   The accompanying notes are an integral part of the consolidated financial
                                  statements.

                                       3
<PAGE>
 
                            WILD OATS MARKETS, INC.
                     CONSOLIDATED STATEMENT OF OPERATIONS
                     (IN THOUSANDS, EXCEPT PER-SHARE DATA)
                                  (UNAUDITED)

<TABLE>
<CAPTION>
 
 
                                                            Three Months Ended               Nine Months Ended
                                                       September 26,   September 27   September 26,    September 27,
                                                            1998           1997            1998            1997
<S>                                                    <C>             <C>            <C>              <C>      
 
Sales                                                        $96,796        $79,955        $287,062          $226,361
Cost of goods sold and occupancy costs                        66,662         55,259         197,486           156,448
                                                             -------        -------        --------           -------
  Gross profit                                                30,134         24,696          89,576            69,913
Operating expenses:
  Direct store expenses                                       20,824         18,582          63,073            52,252
  Selling, general and administrative expenses                 3,632          2,850          11,259             8,939
  Pre-opening expenses                                           802            146           1,783               329
  Non-recurring expenses                                                                        393
                                                             -------        -------        --------           -------
     Income from operations                                    4,876          3,118          13,068             8,393
  Interest income (expense), net                                  76            (16)            600               215
                                                             -------        -------        --------           -------
     Income  before income taxes                               4,952          3,102          13,668             8,608
     Income tax expense                                        1,951          1,270           5,359             3,543
                                                             -------        -------        --------           -------
 
Net income                                                     3,001          1,832           8,309             5,065
                                                             -------        -------        --------           -------
 
Other comprehensive income:
Foreign currency translation adjustment, net                    (113)            (5)            (84)
                                                             -------        -------        --------           -------
 
 
Comprehensive income                                         $ 2,888        $ 1,827        $  8,225          $  5,065
                                                             =======        =======        ========           =======
 
Basic net income per common share                            $  0.23        $  0.17        $   0.64          $   0.49
                                                             =======        =======        ========           =======
 
Diluted net income per common share                          $  0.22        $  0.17        $   0.62          $   0.47
                                                             =======        =======        ========           =======
 
Average common shares outstanding                             13,034         10,557          12,937            10,431
Dilutive effect of stock options                                 390            431             484               307
                                                             -------        -------        --------           -------
Average common shares outstanding assuming dilution           13,424         10,988          13,421            10,738
                                                             =======        =======        ========           =======
 
</TABLE>



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

                                       4
<PAGE>
 
                            WILD OATS MARKETS, INC.
                      CONSOLIDATED STATEMENT OF CASH FLOWS
                                 (In thousands)
                                  (Unaudited)
<TABLE>
<CAPTION>
 
                                                       Nine Months Ended
                                                         September 26,     September 27,
                                                              1998              1997
<S>                                                    <C>                 <C>
 
Cash Flows From Operating Activities
Net income                                                      $  8,309        $  5,065
Adjustments to reconcile net
  income to net cash provided
  by operating activities:
  Depreciation and amortization                                    9,359           6,500
  Loss (gain) on disposal of property and equipment                 (106)           (560)
  Deferred tax provision                                              71           1,544
  Deferred severance payment                                                         476
  Change in assets and liabilities:
     Inventories                                                  (2,105)           (464)
     Receivables and other assets                                   (259)           (462)
     Accounts payable                                              5,022           1,629
     Accrued liabilities                                           5,576             847
                                                                --------        --------
       Net cash provided by operating activities                  25,867          14,575
                                                                --------        --------
 
CASH FLOWS FROM INVESTING ACTIVITIES
Capital expenditures                                             (39,420)        (12,809)
Payment for purchase of acquired
  entities, net of cash acquired                                  (9,585)        (14,003)
Proceeds from sales of equipment                                                     566
                                                                --------        --------
  Net cash used by investing activities                          (49,005)        (26,246)
                                                                --------        --------
 
CASH FLOWS FROM FINANCING ACTIVITIES
Payments on long-term debt                                          (861)         (1,099)
Proceeds from issuance of common stock                             1,517           2,479
                                                                --------        --------
  Net cash provided by financing activities                          656           1,380
                                                                --------        --------
 
Effect of exchange rate changes on cash                              (94)              1
                                                                --------        --------
Net decrease in cash and cash equivalents                        (22,576)        (10,290)
Cash and cash equivalents at beginning of period                  46,686          16,404
                                                                --------        --------
Cash and cash equivalents at end of period                      $ 24,110        $  6,114
                                                                ========        ========
 
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION:
  Cash paid for interest                                        $    237        $    106
                                                                ========        ========                                            

  Cash paid for income taxes                                    $  3,757        $    225
                                                                ========        ========


Supplemental schedule of noncash investing and
 financing activities:
  Short-term note receivable for sale of property               $    365
                                                                ========        
  Acquisition of property with
     seller-financed long-term debt                                             $    480
                                                                                ========
</TABLE> 

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

                                       5
<PAGE>
 
                            WILD OATS MARKETS, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)
                                        
1.   ACCOUNTING POLICIES

     The consolidated balance sheet as of September 26, 1998, the consolidated
     statement of operations for the three and nine months ended September 26,
     1998 and September 27, 1997, as well as the consolidated statement of cash
     flows for the nine months ended September 26, 1998 and September 27, 1997
     have been prepared without an audit. In the opinion of management, all
     adjustments, consisting only of normal, recurring adjustments necessary for
     a fair presentation thereof, have been made.

     Certain information and footnote disclosures normally included in financial
     statements prepared in accordance with generally accepted accounting
     principles have been condensed or omitted.  It is suggested that these
     consolidated financial statements be read in conjunction with financial
     statements and notes thereto included in the Company's 1997 Annual Report
     to Stockholders.  The results of operations for interim periods presented
     are not necessarily indicative of the operating results for the full year.

2.   NEW ACCOUNTING PRONOUNCEMENTS

     In 1997, the Financial Accounting Standards Board ("FASB") issued Statement
     of Financial Accounting Standards ("FAS") No. 130, Reporting Comprehensive
     Income, and FAS No. 131, Disclosure about Segments of an Enterprise and
     Related Information.  The Company adopted FAS No. 130 in 1998, and the
     required presentation is shown in the consolidated balance sheet and
     consolidated statement of operations herein.  The Company will adopt FAS
     No. 131 effective January 3, 1999; however, the Company does not expect FAS
     No. 131 to materially affect financial statement presentation.

     In March 1998, the American Institute of Certified Public Accountants
     ("AICPA") issued Statement of Position ("SOP") 98-1, Accounting for the
     Costs of Computer Software Developed or Obtained for Internal Use.  SOP 98-
     1, which is effective for transactions in fiscal years beginning after
     December 15, 1998, provides guidance on accounting for the costs of
     computer software developed or obtained for internal use.  The Company will
     adopt SOP 98-1 for the 1999 fiscal year, but does not expect such adoption
     to have a material effect on its reported financial results.

     In April 1998, the AICPA issued SOP 98-5, Accounting for the Costs of
     Start-Up Activities.  SOP 98-5 provides guidance on how entities should
     account for pre-opening costs, pre-operating costs, organization costs and
     start-up costs.  SOP 98-5 requires that the costs of start-up activities be
     expensed as incurred.  SOP 98-5 is effective for fiscal years beginning
     after December 15, 1998, and the initial application should be reported as
     a cumulative effect of a change in accounting principle.  The Company will
     adopt SOP 98-5 in fiscal 1999 and does not expect such adoption to have a
     material impact on the Company's results of operations.

     In June 1998, the FASB issued FAS No. 133, Accounting for Derivative
     Instruments and Hedging Activities.  FAS No. 133, which is effective for
     fiscal years beginning after June 15, 1999, requires all derivatives to be
     recognized in the balance sheet as either assets or liabilities and
     measured at fair value.  In addition, all hedging relationships must be
     reassessed and documented pursuant to the provisions of FAS No. 133.  The
     Company will adopt FAS No. 133 for the 2000 fiscal year, but does not
     expect such adoption to materially affect financial statement presentation.

3.  BUSINESS COMBINATIONS

     During the second quarter of 1998, the Company acquired the assets of three
     operating natural foods grocery stores in New York, New York, Santa
     Barbara, California, and Victoria, British Columbia in exchange for $7.4
     million in cash.  The acquisitions were accounted for using the purchase
     method, and the excess cost over the fair value of the net assets acquired
     of $6.3 million was allocated to goodwill, which is being amortized on a
     straight-line basis over 40 years.

     Also during the second quarter of 1998, the Company issued 133,363 shares
     of the Company's common stock in exchange for all of the common stock of
     two companies operating natural foods grocery stores in Columbus, Ohio and
     Little Rock, Arkansas.  The acquisitions were accounted for as poolings of
     interests, and, accordingly, the Company's consolidated financial
     statements for the nine months ended September 26, 1998 include the
     operations of the acquired stores, adjusted to conform with the Company's
     accounting policies and presentation.  The Company's financial statements
     prior to 1998 were not restated based on the immaterial effect of the
     poolings.  Non-recurring, acquisition-related expenses of $393,000 were
     recorded in conjunction with the poolings.

4.  EARNINGS PER SHARE

     Earnings per share are calculated in accordance with the provisions of FAS
     No. 128, Earnings Per Share. FAS No. 128 requires the Company to report
     both basic earnings per share, which is based on the weighted-average
     number of common shares outstanding, and diluted earnings per share, which
     is based on the weighted-average number of common shares outstanding and
     all dilutive potential common shares outstanding, except where the effect
     of their inclusion would be antidilutive (i.e., in a loss period).

                                       6
<PAGE>
 
Item 2.  Management's Discussion and Analysis of Financial Condition and Results
of Operations

This Form 10-Q contains forward-looking statements within the context of Section
21E of the Securities Exchange Act of 1934, as amended.  Each and every forward-
looking statement involves a number of risks and uncertainties, including the
Risk Factors specifically delineated and described in the Company's 1997 Annual
Report to Stockholders and those Risk Factors that have been specifically
expanded or modified below.  The actual results that the Company achieves may
differ materially from any forward-looking statements due to such risks and
uncertainties.  Words such as "believes", "anticipates", "expects", "intends",
and similar expressions are intended to identify forward-looking statements, but
are not the exclusive means of identifying such statements.  The Company
undertakes no obligation to update any forward-looking statements in order to
reflect events or circumstances that may arise after the date of this report.

Certain of the Risk Factors are hereby restated, modified and expanded in
accordance with the following section references that correlate to the
corresponding sections of the Company's 1997 Annual Report to Stockholders:

UNCERTAIN ABILITY TO EXECUTE GROWTH STRATEGY

The Company's business has grown considerably in size and geographic scope,
increasing from 11 stores in 1993, to its current size of 60 stores in 17 states
and Canada.  The Company acquired six operating natural foods stores, opened
five new stores, and relocated one store during the nine months ended September
26, 1998.  The Company also closed two stores in anticipation of relocations to
new sites and sold two stores, both in Colorado, during the nine months ended
September 26, 1998.  During 1997, the Company opened four stores, relocated one
store and acquired nine stores.  The Company's ability to implement its growth
strategy depends to a significant degree upon its ability to open or acquire
stores in existing and new markets and to integrate and operate those stores
profitably.  While the Company plans to expand primarily through the opening of
new stores, it will continue to pursue acquisitions of natural foods retailers
where attractive opportunities exist.  The Company's growth strategy is
dependent upon a number of factors, including its ability to: (i) access
adequate capital resources; (ii) expand into regions where it has no operating
experience; (iii) identify markets that meet its site selection criteria; (iv)
locate suitable store sites and negotiate acceptable lease terms; (v) locate
acquisition targets and negotiate acceptable acquisition terms; (vi) hire, train
and integrate management and store employees; (vii) recruit, train and retain
regional pre-opening and support teams; and (viii) expand its distribution and
other operating systems.  In addition, the Company pursues a strategy of
clustering stores in each of its markets to increase overall sales, achieve
operating efficiencies and further penetrate markets.  In the past, when the
Company has opened a store in a market where it had an existing presence, the
Company has experienced a decline in the sales and operating results at certain
of its existing stores in these markets.  The Company intends to continue to
pursue its store clustering strategy and expects the sales and operating results
trends for other stores in an expanded market to continue to experience
temporary declines related to the clustering of stores.  Further, acquisitions
involve a number of additional risks, such as short-term negative effects on the
Company's reported operating results, diversion of management's attention,
unanticipated problems or legal liabilities, and the integration of potentially
dissimilar operations, some or all of which could have a material adverse effect
on the Company's business, results of operations and financial condition. There
can be no assurance that the Company will achieve its planned expansion in
existing markets, enter new markets, or operate or integrate its existing,
newly-opened or newly-acquired stores profitably.  If the Company fails to do
so, the Company's business, results of operations and financial condition will
be materially and adversely affected.  In addition, the Company's ability to
execute its growth strategy is partially dependent upon the demographic trends
and market conditions in the natural foods industry and any change in those
trends and conditions could adversely affect the Company's future growth rate.

COMPETITION

As Wild Oats enters new geographic markets, its success will depend in part on
its ability to gain market share from established competitors and to compete
effectively with the entry of natural foods grocery competitors and expansion of
natural foods selections by conventional grocers into its existing markets.  The
Company believes its primary competitor in the natural foods grocery store
market is Whole Foods Market, Inc. ("Whole Foods"), a publicly-traded company
based in Texas.  Whole Foods opened a store in Boulder, Colorado in February
1998.  Whole Foods' management has announced that it intends to seek additional
store sites in other cities in which the Company has stores, and has announced
it has acquired sites in Denver, Colorado and Santa Fe, New Mexico, cities in
which the Company has several stores.  If Whole Foods is successful in opening
stores in locations in which the Company has or intends to open stores, the
Company's sales and operating results at such stores may be materially adversely
affected.

FLUCTUATIONS IN FINANCIAL RESULTS

The Company's results of operations may fluctuate significantly from period-to-
period as the result of a variety of factors, including: (i) the number, timing,
mix and cost of store openings, acquisitions or closings; (ii) the ratio of
stores opened to stores acquired; (iii) the opening of stores by the Company or
its competitors in markets where the Company has existing stores; (iv)
comparable store sales results; (v) the ratio of urban format to supermarket
format stores; and (vi) seasonality in sales volume and sales mix in certain
geographic regions.  The Company incurs significant pre-opening expenses, and
new stores typically experience an initial period of operating losses.  As a
result, the opening of a significant number of stores in a single quarter will
have an adverse effect on the Company's results of operations.  Conversely,
delays in opening of planned new stores may result in revenue shortfalls for
both the quarter and the year.  Additionally, the opening of competing stores
may have a similar adverse effect on results of operations. Due to the foregoing
factors, the Company believes that period-to-period comparisons of its operating
results are not necessarily meaningful and that such comparisons cannot be
relied upon as indicators of future financial performance.

A variety of factors affect the Company's comparable store sales results,
including, among others, the relative proportion of new stores to mature stores,
the opening of stores by the Company or its competitors in markets where the
Company has existing stores, the timing of promotional events, the Company's
ability to execute its operating strategy effectively, changes in consumer

                                       7
<PAGE>
 
preferences for natural foods and general economic conditions.  Past increases
in comparable store sales may not be indicative of future performance.  The
Company's comparable store sales results have been negatively affected in the
past by planned cannibalization (the loss of sales at an existing store when the
Company opens a new store nearby) resulting from the implementation of the
Company's store clustering strategy.  The Company expects that comparable store
sales increases have been or will continue to be negatively affected by planned
cannibalization in the fourth quarter of 1998 and throughout 1999 due to the
planned opening of new stores in several of the Company's existing markets
including Santa Monica, California and Denver, Colorado in 1998 and Phoenix,
Arizona, Kansas City, Missouri, St. Louis, Missouri, Las Vegas, Nevada and
Albuquerque, New Mexico, in 1999.  There can be no assurance that comparable
store sales for any particular period will not decrease in the future.

GOVERNMENT REGULATION

The Company is subject to numerous federal, state and local laws, regulations
and ordinances regulating health and sanitation standards, food labeling and
handling, equal employment, minimum wages and licensing for the sale of food and
alcoholic beverages. Difficulties or failures in complying with these
regulations could adversely affect the operations of an existing store or delay
the opening of a new store.

In December 1997, the United States Department of Agriculture ("USDA")
published, pursuant to the Organic Food Production Act of 1990, its proposed
National Organic Program rules, under which the USDA proposes to regulate the
production, handling, labeling and sale of products bearing the "organic" label.
The Company believes that the rules as published substantially weaken the
current standards for organic food production and labeling, and may undermine
consumer confidence in the quality of certain of the foods sold in its stores.
The rules also may add additional expense to the Company's cost of private label
and in-store prepared foods sold by the Company.  The Company submitted a
detailed response to the USDA during the comment period.  If the rules are
adopted as currently proposed, such rules could have an adverse effect on the
Company's business, results of operations and financial condition.

In April 1998, the United States Food and Drug Administration ("FDA") published
a proposed amendment to the Dietary Supplement Health and Education Act of 1994.
The Company believes the proposed amendments could substantially limit the
consumer's access to important information on vitamins and supplements.  The
Company submitted a response to the proposed amendment before the end of the FDA
comment period.  If the proposed amendments are adopted as currently drafted,
information about, and perhaps access to, vitamins and supplements could be
restricted, which could have an adverse effect on the Company's business,
results of operations and financial condition.

OWNERSHIP AND SALE OF REAL PROPERTY

The Company has purchased, or entered into contracts to purchase, parcels of
real property for the construction or remodeling of new stores or the relocation
of existing stores.  The Company also purchased a ground lease on undeveloped
real property.  The Company has constructed two, and intends to construct or
remodel two more new stores on real property purchased or leased by the Company.
There can be no assurance that the Company will be successful in constructing
the planned stores within the Company's projected budgets or on the schedules
currently anticipated.  Failure to complete these projects on time or within
budget could have a material adverse impact on the Company's business, results
of operations, including delays in realizing sales revenues, and financial
condition.  The Company anticipates that, after construction or remodeling of
stores on certain of the acquired properties is completed, it will sell the land
and buildings in one or more sale-leaseback transactions under which the Company
will lease the stores from the purchaser of the property.  There can be no
assurance that the Company will be successful in locating and negotiating
acceptable transactions with one or more parties for the sale-leaseback of the
properties currently owned by the Company, which may result in unplanned long-
term uses of the Company's cash that would otherwise be available to fund
operations.

                                       8
<PAGE>
 
Results of Operations

The following table sets forth, for the periods indicated, certain selected
income statement data expressed as a percentage of sales:

<TABLE>
<CAPTION>
 
 
                                                      Three Months Ended              Nine Months Ended
                                                September 26,   September 27,   September 26,   September 27,
                                                     1998            1997            1998            1997
<S>                                             <C>             <C>             <C>             <C>
 
Sales                                                   100.0%          100.0%          100.0%          100.0%
Cost of goods sold and occupancy costs                   68.9            69.1            68.8            69.1
                                                        -----           -----           -----           -----
Gross margin                                             31.1            30.9            31.2            30.9
Direct store expenses                                    21.5            23.2            22.0            23.1
Selling, general and administrative expenses              3.8             3.6             3.9             4.0
Pre-opening expenses                                      0.8             0.2             0.6             0.1
Non-recurring expenses                                                                    0.1
                                                        -----           -----           -----           -----
Income from operations                                    5.0             3.9             4.6             3.7
Interest income, net                                      0.1                             0.2             0.1
                                                        -----           -----           -----           -----
Income before income taxes                                5.1             3.9             4.8             3.8
Income tax expense                                        2.0             1.6             1.9             1.6
                                                        -----           -----           -----           -----
Net income                                                3.1%            2.3%            2.9%            2.2%
                                                        =====           =====           =====           =====
 
</TABLE>

STORE OPENINGS, CLOSINGS, REMODELS, RELOCATIONS AND ACQUISITIONS.  During the
third quarter of 1998, the Company opened two new stores in Miami Beach, Florida
and Santa Monica, California.  During the nine months ended September 26, 1998,
the Company opened five stores and acquired six stores, one each in Columbus,
Ohio (which was subsequently relocated), Nashville, Tennessee, New York, New
York, Victoria, British Columbia, Santa Barbara, California and Little Rock,
Arkansas, and sold two stores in Colorado.  The Company closed two stores in
anticipation of relocations to new sites.  The Company plans to open as many as
three additional new stores and relocate two stores during the remainder of
1998.  The Company anticipates that it also may acquire one or more operating
natural foods grocery stores during the remainder of 1998.  The Company's
results of operations have been and will continue to be affected by, among other
things, the number, timing and mix of store openings, acquisitions or closings.
New stores build their sales volumes and refine their merchandise selection
gradually and, as a result, generally have lower gross margins and higher
operating expenses as a percentage of sales than more mature stores.  The
Company anticipates that the new stores opened in 1998 will experience operating
losses for the first six to 12 months of operation, in accordance with historic
trends.  Further, acquired stores, while generally profitable as of acquisition
date, generate lower gross margins and store contribution margins than the
Company average, due to their substantially lower volume purchase discounts.
Over time, typically six months, as the Company sells through the acquired
inventories and implements its volume purchase discounts, the Company expects
that the gross margin and store contribution margin of the acquired stores will
approach the Company average.  The Company anticipates that a high concentration
of acquired stores will have a temporary negative impact on the Company's
consolidated gross margin and store contribution margin.

The Company is actively upgrading, remodeling or relocating some of its older
stores.  Remodels and relocations typically cause short-term disruption in sales
volume and related increases in certain expenses as a percentage of sales, such
as payroll.  Remodels on average take between 90 and 120 days to complete.  The
Company cannot predict whether sales disruptions and the related impact on
earnings may be greater in time or volume than projected in certain remodeled or
relocated stores.  The Company will continue to evaluate the profitability of
all of its stores on an ongoing basis and may, from time to time, make decisions
regarding closures, disposals, relocations or remodels in accordance with such
evaluations.  As part of this strategy, during the first nine months of 1998,
the Company sold two stores in Colorado, consolidated its stores in Fort
Collins, Colorado by closing one store located there, relocated one store in
Columbus, Ohio, and closed one store in Denver, Colorado in anticipation of a
relocation in the fourth quarter of 1998.

Subsequent to the third quarter of 1998, the Company introduced its Internet
shopping website, "shop.wildoats.com".  The Company incurred and will continue
to incur selling, general and administrative costs for the purchase of the
software, advertising and personnel to operate the website.  The Company
anticipates that the website will experience small operating losses or break
even on expenses for the first 12 months of operation until consumer awareness,
acceptance and use of the website grow.

SALES.  Sales for the three months ended September 26, 1998 increased 21% to
$96.8 million from $80.0 million for the same period in 1997.  Sales for the
nine months ended September 26, 1998 increased 27% to $287.1 million from $226.4
million for the same period in 1997.  The increases were primarily due to the
opening of five new stores and the acquisition of six stores, and the relocation
of one store in the first nine months of 1998, and the inclusion of four new
stores opened, one relocated store, and nine stores acquired in 1997.
Comparable store sales increased 4% for the third quarter of 1998 and 4% for the
first nine months of 1998, based on both new and acquired stores that have been
operating longer than 12 months.  The Company expects its comparable store sales
increases to be 5% to 6% in the fourth quarter of 1998.  Sales in the third
quarter were slightly lower than originally projected because of unexpected
construction delays in the opening of two of the Company's stores.  See "Risk
Factors--Fluctuations in Financial Results".

GROSS PROFIT. Gross profit for the three months ended September 26, 1998
increased 22% to $30.1 million from $24.7 million for the same period in 1997.
Gross profit for the nine months ended September 26, 1998 increased 28% to $89.6
million from $69.9 

                                       9
<PAGE>
 
million for the same period in 1997. The increases in gross profit are primarily
attributable to the increase in the number of stores operated by the Company.
Gross profit as a percentage of sales for the three months ended September 26,
1998 increased to 31.1% from 30.9% for the same period in 1997. Gross profit as
a percentage of sales for the nine months ended September 26, 1998 increased to
31.2% from 30.9% for the same period in 1997. The increases are primarily
attributable to the maturation of the Company's store base, the Company's volume
purchase discounts, and enhanced inventory management.

DIRECT STORE EXPENSES.  Direct store expenses for the three months ended
September 26, 1998 increased 12% to $20.8 million from $18.6 million for the
same period in 1997.  Direct store expenses for the nine months ended September
26, 1998 increased 21% to $63.1 million from $52.3 million for the same period
in 1997.  The increases in direct store expenses are attributable to the
increase in the number of stores operated by the Company.  Direct store expenses
as a percentage of sales for the three months ended September 26, 1998 decreased
to 21.5% from 23.2% for the same period in 1997.  Direct store expenses as a
percentage of sales for the nine months ended September 26, 1998 decreased to
22.0% from 23.1% for the same period in 1997.  The decreases are due to the
matured performance of the new stores opened in 1997, as well as improved
control of direct store expenses, particularly payroll and benefits costs.

SELLING, GENERAL AND ADMINISTRATIVE EXPENSES.  Selling, general and
administrative expenses for the three months ended September 26, 1998 increased
27% to $3.6 million from $2.9 million for the same period in 1997.  Selling,
general and administrative expenses for the nine months ended September 26, 1998
increased 26% to $11.3 million from $8.9 million for the same period in 1997.
Selling, general and administrative expenses as a percentage of sales for the
three months ended September 26, 1998 increased to 3.8% from 3.6% for the same
period in 1997.  The increase is the result of additional central and regional
support staff and infrastructure that the Company has added to support its
increased number of stores.  Selling, general and administrative expenses as a
percentage of sales for the nine months ended September 26, 1998 remained
relatively constant at 3.9% versus 4.0% for the same period in 1997.  Selling,
general and administrative expenses have been running higher than expected in
the first nine months of 1998 due to additional personnel costs in the
information technology, marketing and purchasing departments needed to support
the Company's growth plans, as well as additional costs to distribute the
Company's marketing materials, such as its specials flyers, to its customers.
The Company anticipates that the higher levels of selling, general and
administrative expenses will continue through 1998.  In addition, the Company
moved its corporate office subsequent to the third quarter of 1998 to a larger
facility to accommodate an increased support staff for its larger base of
stores.  There will be additional selling, general and administrative expenses
for rent and utilities on the new facility, and the costs of relocating the
information systems currently used by the Company.

PRE-OPENING EXPENSES.   Pre-opening expenses for the three months ended
September 26, 1998 increased 449% to $802,000 from $146,000 for the same period
in 1997.  Pre-opening expenses as a percentage of sales for the three months
ended September 26, 1998 increased to 0.8% from 0.2% for the same period in
1997.  The increases are primarily due to the delayed opening of one store,
resulting in additional pre-opening costs in the form of rental payments, as
well as the opening of two new stores in the third quarter of 1998 as compared
to one new store in the same period in 1997.   Pre-opening costs for the nine
months ended September 26, 1998 increased 442% to $1.8 million from $329,000 for
the same period in 1997.  For the nine months ended September 26, 1998, pre-
opening costs as a percentage of sales increased to 0.6% from 0.1% due to the
opening of five new stores and the relocation of one store in the first nine
months of 1998 as compared to the opening of two new stores in the same period
in 1997.

NON-RECURRING EXPENSES.  In conjunction with the Company's pooling-of-interests
transactions during the nine months ended September 26, 1998, the Company
recorded a non-recurring charge of $393,000.  The charge is attributable to
severance costs, lease termination costs, and asset write-downs.

NET INTEREST INCOME.  Net interest income for the three months ended September
26, 1998 was $76,000 as compared to net interest expense of $16,000 for the same
period in 1997.  Net interest income for the nine months ended September 26,
1998 increased 179% to $600,000 from $215,000 for the same period in 1997.  Net
interest income as a percentage of sales for the three months ended September
26, 1998 increased to 0.1% from net interest expense for the same period in
1997.  Net interest income as a percentage of sales for the nine months ended
September 26, 1998 increased to 0.2% from 0.1% for the same period in 1997.  The
change is attributable to the investment of the net proceeds from the Company's
public offerings in December 1997 and October 1996 and to lower levels of
indebtedness incurred to fund new store openings and acquisitions.

LIQUIDITY AND CAPITAL RESOURCES

The Company's primary sources of capital have been cash flow from operations,
trade payables, bank indebtedness, and the sale of equity securities.  Primary
uses of cash have been the financing of new store development, new store
openings, acquisitions and purchases of real property.

Net cash provided by operating activities was $25.9 million during the nine
months ended September 26, 1998 as compared to $14.6 million during the same
period in 1997.  Cash provided by operating activities increased during this
period primarily due to increases in net income before depreciation and
amortization expense and increases in accounts payable and accrued liabilities.
The Company has not required significant external financing to support inventory
requirements at its existing and new stores because it has been able to rely on
vendor financing for most of the inventory costs, and anticipates that vendor
financing will continue to be available for new store openings.  The Company
also realized gains from the sale by the Company of certain rights in real
property in the third quarter of 1998.

Net cash used by investing activities was $49.0 million during the nine months
ended September 26, 1998 as compared to $26.2 million during the same period in
1997.  The increase is due to the opening of five new stores, the acquisition of
six stores, the relocation of one store, the purchase of certain parcels of real
property, and several store remodels in the first nine months of 1998 as 

                                       10
<PAGE>
 
well as the construction costs incurred for six new stores and relocations now
under construction which are expected to open in the remainder of 1998 or early
1999, as compared to two new stores and nine acquired stores in the first nine
months of 1997.

Net cash provided by financing activities was $656,000 during the nine months
ended September 26, 1998 as compared to $1.4 million during the same period in
1997.  The change reflects reduced long-term debt and decreased issuance of
common stock upon the exercise of employee stock options during the first nine
months of 1998.

The Company has a revolving line of credit of $40.0 million.  The facility has a
seven-year term and bears interest, at the Company's option, at the prime rate
or LIBOR plus 1.25%.  The line of credit agreement includes certain financial
and other covenants, as well as restrictions on payments of dividends.  As of
November 4, 1998, there were no borrowings outstanding under this facility.

The Company spent approximately $12.6 million during the third quarter of 1998
for new store development, remodels and maintenance capital expenditures,
exclusive of any acquisitions.  The Company anticipates that it will spend
approximately $45.0 million during 1998 for real property purchases, new store
development, remodels and maintenance capital expenditures, exclusive of any
acquisitions.  Three new store openings and two store relocations are planned
for the remainder of 1998.  The Company's average capital expenditures to open a
store, including leasehold improvements, equipment and fixtures, have ranged
from approximately $1.0 million to $3.0 million over the past 24 months,
excluding inventory costs and initial operating losses.  The Company expects to
increase the average size of its new stores and increase the number of its new
store openings over time, and is using a greater proportion of new and custom
equipment in its stores.  Therefore, the Company anticipates that its average
capital expenditures per store will increase over time by approximately
$500,000.

The Company has purchased, or entered into contracts to purchase, real property
or ground leases on which it intends to construct new stores or relocate certain
existing stores.  The Company constructed one new store that opened in March
1998, has constructed one store planned to open in the fourth quarter of 1998,
is constructing a third store planned to open in the first quarter of 1999, and
plans to commence remodeling of one additional new store in early 1999.
Construction of stores requires substantially greater cash outlays than the
remodeling of existing buildings (i.e., $3.5 to $7.0 million as compared to $1.0
to $3.0 million).  The Company intends to sell certain of the acquired real
properties in one or more sale-leaseback transactions in order to recover the
cash expended for the purchase of the underlying real property and the building
construction costs.  If the Company is not successful in locating and
negotiating acceptable transactions with one or more parties for the sale and
leaseback of certain of the properties currently owned by the Company, this may
result in unplanned, long-term uses of the Company's cash that otherwise would
be available to fund operations.  Additionally, unexpected permitting and
construction delays could result in greater or longer-term cash outlays.  Delays
in opening new stores also may result in reductions in forecasted sales revenues
from projected levels and increases in pre-opening costs for any given reporting
period.

The cost of initial inventory for a new store has historically been
approximately $500,000; however, the Company relies on vendor financing for most
of this cost.  Pre-opening costs currently are approximately $250,000 to
$300,000 per store and are expensed when the new store opens.  Beginning in 1999
pre-opening costs will be expensed as incurred.  The amounts and timing of such
pre-opening costs will depend upon the availability of new store sites and other
factors, including the location of the store and whether it is in a new or
existing market for the Company, the size of the store, and the required build-
out at the site.  Costs to acquire future stores, if any, are impossible to
predict and could vary materially from the cost to open new stores. There can be
no assurance that actual capital expenditures will not exceed anticipated
levels.  The Company believes that the net proceeds of its public stock offering
in December 1997, together with cash generated from operations and funds
available under the revolving line will be sufficient to satisfy its cash
requirements, exclusive of acquisitions, through 1998 and 1999.

YEAR 2000 ISSUES

As the Year 2000 approaches, the Company recognizes the need to ensure its
operations will not be adversely impacted by Year 2000 software or hardware
failures.  The Company has determined that, with the exception of the Company's
current headquarters voicemail system, all of its major software and hardware
systems at its corporate headquarters are Year 2000 compliant.  The cost for a
Year 2000-compliant voicemail system is not material.  The Company has
substantially completed installing point-of-sale hardware (cash registers and
scanners) in its stores that are Year 2000 compliant.  Total replacement and
installation cost to date has been approximately $1 million, with the cost to
complete the installation in 1999 estimated at an additional $300,000.  The
existing point-of-sale hardware was and is being replaced to accommodate a
merchandise management system that is Year 2000 compliant and that was
previously acquired by the Company for its greater item movement, tracking,
pricing and reporting capabilities.

The Company also is in the process of verifying whether its major suppliers,
service providers, and financial institutions are Year 2000 compliant.  Many of
the Company's product vendors are smaller businesses that have not considered
the impact of Year 2000 noncompliance and so are taking no steps to ensure
compliance.  To the extent that product vendors' manufacturing or distribution
systems fail as a result of Year 2000 noncompliance, certain products carried by
the Company's stores could become unavailable, resulting in decreases in
operating revenues, although in many circumstances, alternative local vendors'
products may be available.  The Company's stores' operations could be materially
adversely affected if utilities are disrupted.  At this time the Company has not
developed any contingency plans to address product or utility disruptions.  One
of the Company's larger distributors has disclosed that certain of its warehouse
facilities' systems are not Year 2000 compliant, but that it will be purchasing
compliant systems in 1998 and 1999.  The Company cannot currently evaluate the
magnitude of the impact that a failure by the distributor to install compliant
systems could have on the Company's operations.  A failure in the distributor's
warehouse facilities could affect the Company's ability to stock product in
certain of its stores, resulting in lower sales revenues in those stores.  If
the Company's financial institutions are not Year 2000 compliant, a failure in
their operating system could result in a temporary inability by the Company to
access necessary cash resources required for operations; however, normal store
operations will generate sufficient revenues to cover daily operating needs.
The Company has commenced review of the various individual mechanical systems,
such 

                                       11
<PAGE>
 
as HVAC, refrigeration and security systems, in its stores to determine whether
any Year 2000 compliance issues exist as to these systems. The Company will
contact the suppliers of certain store systems where Year 2000 compliance may be
an issue to obtain confirmation of compliance or instructions for reprogramming
in the event of a compliance problem. The Company does not anticipate that any
major store systems will require replacement because of Year 2000 compliance
concerns or that noncompliance of any mechanical systems will have any material
effect on store operations. The proportion of perishable goods that could be
impacted by a failure in refrigerated systems is small on a total dollar basis
to the gross inventory of any store. The Company will continue to make certain
investments in its software systems and applications to ensure that they are
Year 2000 compliant. The financial impact to the Company is not anticipated to
be material in any single year.

The estimates and conclusions regarding Year 2000 impact contained above are
forward-looking statements based on the Company's best estimates of future
events.  Actual results may differ due to certain risks and uncertainties.

NEW ACCOUNTING PRONOUNCEMENTS

In 1997, the Financial Accounting Standards Board ("FASB") issued Statement of
Financial Accounting Standards ("FAS") No. 130, Reporting Comprehensive Income.
FAS No. 130 establishes standards for the reporting and presentation of
comprehensive income and its components in a full set of general-purpose
financial statements.  FAS No. 130 requires that all items that are required to
be recognized under accounting standards as components of comprehensive income
be reported in a financial statement that is displayed with the same prominence
as other financial statements.  The Company adopted FAS No. 130 in 1998.

Also in 1997, the FASB issued FAS No. 131, Disclosure about Segments of an
Enterprise and Related Information.  FAS No. 131 revises the current
requirements for reporting business segments by redefining such segments
according to management's disaggregation of the business for purposes of making
operating decisions and allocating internal resources.  The Company will adopt
FAS No. 131 effective January 2, 1999; however, the Company does not expect FAS
No. 131 to materially affect financial statement presentation.

In March 1998, the American Institute of Certified Public Accountants ("AICPA")
issued Statement of Position ("SOP") 98-1, Accounting for the Costs of Computer
Software Developed or Obtained for Internal Use.  SOP 98-1, which is effective
for transactions in fiscal years beginning after December 15, 1998, provides
guidance on accounting for the costs of computer software developed or obtained
for internal use.  The Company will adopt SOP 98-1 for the 1999 fiscal year, but
does not expect such adoption to have a material effect on its reported
financial results.

In April 1998, the AICPA issued SOP 98-5, Accounting for the Costs of Start-Up
Activities.  SOP 98-5 provides guidance on how entities should account for
start-up costs, such as pre-opening costs, pre-operating costs, organization
costs and start-up costs.  SOP 98-5 requires that the costs of start-up
activities be expensed as incurred.  SOP 98-5 is effective for fiscal years
beginning after December 15, 1998, and the initial application should be
reported as a cumulative effect of a change in accounting principle.  The
Company will adopt SOP 98-5 in fiscal 1999 and does not expect adoption to have
a material effect on the Company's results of operations.

In June 1998, the FASB issued FAS No. 133, Accounting for Derivative Instruments
and Hedging Activities.  FAS No. 133, which is effective for fiscal years
beginning after June 15, 1999, requires all derivatives to be recognized in the
balance sheet as either assets or liabilities and measured at fair value.  In
addition, all hedging relationships must be reassessed and documented pursuant
to the provisions of FAS No. 133.  The Company will adopt FAS No. 133 for the
2000 fiscal year, but does not expect such adoption to materially affect
financial statement presentation.

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Not applicable.

                                       12
<PAGE>
 
PART II.  OTHER INFORMATION

ITEM 1.  LEGAL PROCEEDINGS


Alfalfa's Canada, Inc., the Company's Canadian subsidiary, is a defendant in a
suit brought in the Supreme Court of British Columbia, by one of its
distributors, Waysafer Wholefoods Limited and one of its principals, seeking
monetary damages for breach of contract and injunctive relief to enforce a
buying agreement for the three Canadian stores entered into by a predecessor of
Alfalfa's Canada, Inc.  Under the buying agreement, the stores must buy products
carried by the plaintiff if such are offered at the current advertised price of
its competitors. The suit was filed in September 1996.  In June 1998, the
Company filed a Motion for Dismissal on the grounds that the contract in dispute
constituted a restraint of trade.  The Motion was subsequently denied.  The
Company does not believe its potential exposure in connection with the suit to
be material.  There are no other material pending legal proceedings to which the
Company or its subsidiaries are a party.  From time to time, the Company is
involved in lawsuits that the Company considers to be in the normal course of
its business.

ITEM 2.  CHANGES IN SECURITIES

Not applicable.


ITEM 3.  DEFAULTS UPON SENIOR SECURITIES

Not applicable.


ITEM 4.  SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

Not applicable.


ITEM 5.  OTHER INFORMATION

Not applicable.

ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

  (a)  Exhibits

  EXHIBIT
  Number      DESCRIPTION OF DOCUMENT
  ------      -----------------------

  3(i).1.(a)  Amended and Restated Certificate of Incorporation of Registrant.*

  3(i).1.(b)  Certificate of Correction to Amended and Restated Certificate of
              Incorporation of the Registrant.*

  3(ii).1     Amended and Restated By-Laws of Registrant.*

  4.1         Reference is made to Exhibits 3(i).1 through 3(ii).1.*

  4.2         Rights Agreement dated as of May 22, 1998 between Registrant and
              Norwest Bank Minnesota N.A.**

  10.1        Employment Agreement dated March 2, 1998 between Registrant and
              John Weber.

  27.1        Financial Data Schedule.

*   Incorporated by reference to the Company's Annual Report on Form 10-K for
the year ended December 27, 1997 (File Number 0-21577).

**  Incorporated by reference to the Company's Registration Statement on Form 8-
A dated May 21, 1998.

  (b)  Reports on Form 8-K.

  The Company did not file a Form 8-K during the three-month period ended
September 26, 1998.

                                       13
<PAGE>
 
                                   SIGNATURES

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, in the City of Boulder, County of
Boulder, State of Colorado, on the 11th day of November 1998.

  WILD OATS MARKETS, INC.



                                     By  /s/  Mary Beth Lewis
                                         --------------------
                                         Mary Beth Lewis
                                         Executive Officer, Vice President of
                                         Finance, Treasurer and Chief Financial
                                         Officer
                                         (Principal Financial and Accounting
                                         Officer)

                                       14