<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-Q/A

[X]   QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
      SECURITIES EXCHANGE ACT OF 1934
      FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 29, 2000

[ ]   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
      SECURITIES EXCHANGE ACT OF 1934
      FOR THE TRANSITION PERIOD FROM ______ TO ______

COMMISSION FILE NUMBER 0-19952

                                 CHRONIMED INC.
             (Exact name of registrant as specified in its charter)


      MINNESOTA                                                 41-1515691
--------------------------------------------------------------------------------
(State or other jurisdiction of                             (I.R.S. Employer
 incorporation or organization)                           Identification Number)

                             10900 RED CIRCLE DRIVE
                           MINNETONKA, MINNESOTA 55343
                    (Address of principal executive offices)
                                   (Zip Code)

        Registrant's telephone number, including area code (952) 979-3600

                     --------------------------------------

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

Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date.

      Common Stock, $.01 par value -  12,147,021 shares outstanding as of
November 7, 2000



<PAGE>   2
                                INTRODUCTORY NOTE

The purpose of this Form 10-Q/A is to restate the quarterly condensed
consolidated financial statements for the quarters ended September 29, 2000 and
October 1, 1999 for Chronimed Inc. ("Chronimed" or the "Company") (see Note H to
the Condensed Consolidated Financial Statements). The Company issued press
releases on June 14, 2001 and June 21, 2001, which it filed as exhibits to Form
8-K dated the same dates, relating to its intention to restate certain of its
financial statements. The Company is concurrently filing a Form 10-K for its
fiscal year ended June 29, 2001 that includes restated financial statements for
fiscal year 2000, and a Form 10-Q/A for each of the quarterly periods September
29, 2000, December 29, 2000, and March 29, 2001.

The matters relating to the restatement referenced in the 2001 Form 10-K have a
financial statement impact for the periods covered by this 10-Q/A as follows:

Revenue--For the quarter ended October 1, 1999, decrease revenue by $827,000.
For the quarter ended September 29, 2000, decrease revenue by $1.6 million.

Bad debt expense--For the quarter ended September 29, 2000 increase bad debt
expense by $989,000. There was no restatement of bad debt expense for the
quarter ended October 1, 1999.

Net Income from Continuing Operations--For the quarter ended October 1, 1999,
decrease net income by $504,000. For the quarter ended September 29, 2000,
decrease net income before taxes by $1.6 million.

Accounts Receivable--At June 30, 2000 reduce accounts receivable by $7.6
million. At September 29, 2000 reduce accounts receivable by $10.2 million.

Income Taxes Receivable/Payable--At June 30, 2000 increase income taxes
receivable by $1.1 million. At September 29, 2000 increase income taxes
receivable by $2.9 million.

Deferred tax assets--At June 30, 2000 increase deferred tax assets by $1.8
million. At September 29, 2000 increase deferred tax assets by $1.1 million.

The principal effects of the change on the accompanying financial statements are
presented in Note H to the Condensed Consolidated Financial Statements

For purposes of this Form 10-Q/A, and in accordance with rule 12b-15 under the
Securities and Exchange Act of 1934, as amended, the Company has amended and
restated in its entirety each item of the Company's Form 10-Q for the quarterly
periods ended September 29, 2000, which has been affected by the restatement.
This Form 10-Q/A does not reflect events occurring after the filing of the
original Form 10-Q, or modify or update those disclosures in any way, except as
required to reflect the effects of this restatement.


                                       1
<PAGE>   3

                                      INDEX

                         CHRONIMED INC. AND SUBSIDIARIES



PART I.  FINANCIAL INFORMATION


Item 1.  Financial Statements (as restated)

                 Consolidated Balance Sheets - September 29, 2000 (Unaudited)
                 and June 30, 2000

                 Consolidated Statements of Operations (Unaudited) - Three
                 months ended September 29, 2000 and October 1, 1999

                 Consolidated Statements of Cash Flows (Unaudited) - Three
                 months ended September 29, 2000 and October 1, 1999

                 Notes to Consolidated Financial Statements - September 29, 2000


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


Item 3.  Quantitative and Qualitative Disclosures About Market Risk


PART II. OTHER INFORMATION

Items 1, 2, 3, 4 and 5 required under Part II have been omitted since all items
are not applicable or the answers are negative.

Item 6.  Exhibits and Reports on Form 8-K

         a.)     Exhibits

         b.)     Reports on Form 8-K


SIGNATURES


                                       2
<PAGE>   4

PART I.  FINANCIAL INFORMATION
Item 1.  FINANCIAL STATEMENTS


                                 CHRONIMED INC.
                           CONSOLIDATED BALANCE SHEETS
                                 (In thousands)

<TABLE>
<CAPTION>

                                                                     SEPTEMBER 29,            JUNE 30,
                                                                    2000 (UNAUDITED)           2000
                                                                    ----------------      --------------
                                                                     (As restated)         (As restated)
<S>                                                                   <C>                   <C>
ASSETS
Current assets
  Cash and cash equivalents                                             $    187              $     --
  Available-for-sale securities                                               --                    --
  Accounts receivable (net of allowance of $9,936                         35,736                39,762
      at September 29, 2000, and $8,459 at June 30, 2000)
  Income taxes receivable                                                  3,145                 1,901
  Inventory                                                                6,149                 6,111
  Other current assets                                                       874                   848
  Deferred taxes                                                           2,363                 3,144
                                                                        --------              --------
    Total current assets                                                  48,454                51,766

Property and equipment
  Property and equipment                                                  14,077                14,889
  Allowance for depreciation                                              (7,632)               (8,338)
                                                                        --------              --------
                                                                           6,445                 6,551

Goodwill, net                                                              8,620                 9,031
Net assets of discontinued operations                                     10,554                10,465
Deferred taxes                                                               508                   508
Other assets                                                                 130                   109
                                                                        --------              --------
  Total assets                                                          $ 74,711              $ 78,430
                                                                        ========              ========

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities
  Accounts payable                                                        10,483                10,507
  Accrued expenses                                                         1,788                 2,366
  Short-term debt                                                             --                 2,500
                                                                        --------              --------
    Total current liabilities                                             12,271                15,373

Shareholders' equity
  Preferred Stock                                                             --                    --
  Common Stock, issued and outstanding shares--
    12,147 and 12,147 respectively                                           121                   121
  Additional paid-in capital                                              52,839                52,839
  Retained earnings                                                        9,401                 9,641
                                                                        --------              --------
                                                                          62,361                62,601
  Accumulated other comprehensive income --
   Unrealized (loss) gain on available-for-sale securities                    79                   456
                                                                        --------              --------
    Total shareholders' equity                                            62,440                63,057

                                                                        --------              --------
Total liabilities and shareholders' equity                              $ 74,711              $ 78,430
                                                                        ========              ========
</TABLE>


See notes to consolidated financial statements

                                       3
<PAGE>   5

                                 CHRONIMED INC.
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
                                   (Unaudited)

<TABLE>
<CAPTION>

                                                                          THREE MONTHS ENDED
                                                             -----------------------------------------
                                                                SEPTEMBER 29,             OCTOBER 1,
                                                                    2000                     1999
                                                             -------------------       ---------------
                                                               (As restated)             (As restated)
<S>                                                             <C>                      <C>
REVENUE
  Mail Order                                                      $ 34,839                 $ 26,833
  Retail                                                            28,005                   23,218
                                                                  --------                 --------
    Total Revenue                                                   62,844                   50,051
            Yr to Yr Growth                                           25.6%                    41.5%
COSTS AND EXPENSES
  Cost of revenue                                                   54,696                   41,963
    Gross profit                                                     8,148                    8,088
             % of Revenue                                             13.0%                    16.2%

  Selling and marketing                                              1,105                    1,194
  General and administrative                                         7,121                    7,171
  Bad debt expense                                                   1,075                      704
                                                                  --------                 --------
    Total operating expenses                                         9,301                    9,069
             % of Revenue                                             14.8%                    18.1%

(LOSS) FROM OPERATIONS                                              (1,153)                    (981)
             % of Revenue                                             -1.8%                    -2.0%

  Interest income                                                       50                       --
  Interest (expense)                                                   (48)                     (23)
  Other income                                                          21                       --
                                                                  --------                 --------

(LOSS) BEFORE INCOME TAXES                                          (1,130)                  (1,004)
  Income tax benefit                                                   426                      392

(LOSS) FROM CONTINUING OPERATIONS                                     (704)                    (612)
             % of Revenue                                             -1.1%                    -1.2%

INCOME FROM DISCONTINUED OPERATIONS, NET OF TAX                        464                      436
                                                                  --------                 --------

NET (LOSS)                                                        $   (240)                $   (176)
                                                                  ========                 ========
             % of Revenue                                             -0.4%                    -0.4%


BASIC AND DILUTED EARNINGS (LOSS) PER SHARE
  Loss from Continuing Operations                                    (0.06)                   (0.05)
  Income from Discontinued Operations                                 0.04                     0.04
                                                                  --------                 --------
  Net (Loss) per share                                            $  (0.02)                $  (0.01)
                                                                  ========                 ========


WEIGHTED AVERAGE SHARES OUTSTANDING                                 12,147                   12,096
</TABLE>


See notes to consolidated financial statements

                                       4
<PAGE>   6
                                 CHRONIMED INC.
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                   (Unaudited)

<TABLE>
<CAPTION>

                                                                                  THREE MONTHS ENDED
                                                                        -------------------------------------
                                                                           SEPTEMBER 29,          OCTOBER 1,
                                                                               2000                  1999
                                                                        ----------------       --------------
                                                                          (As restated)        (As restated)
<S>                                                                       <C>                  <C>
OPERATING ACTIVITIES
  Net income (loss)                                                         $  (240)             $  (176)
  Less income/gain from discontinued operations                                 464                  436

    (Loss) from continuing operations                                          (704)                (612)

  Adjustments to reconcile income from continuing operations
    to net cash used in operating activities:
      Depreciation and amortization                                             871                1,073
      Deferred income taxes                                                     781                  (57)
      Gain on sale of business                                                  (22)                  --
      Changes in operating assets and liabilities:
        Accounts receivable                                                   2,021               (5,137)
        Income taxes                                                         (1,244)              (1,187)
        Inventory                                                              (470)                (621)
        Accounts payable                                                        (24)               2,072
        Accrued expenses                                                       (692)              (1,354)
        Other assets                                                           (264)                (480)
                                                                            -------              -------
      Net cash provided by (used in) operating activities                       253               (6,303)

INVESTING ACTIVITIES
  Proceeds from sale of Home Service Medical Business                         3,000                   --
  Purchases of property and equipment                                          (566)                (503)
                                                                            -------              -------
      Net cash provided by (used in) investing activities                     2,434                 (503)

FINANCING ACTIVITIES
  Net proceeds from issuance of Common Stock                                     --                    8
  Net (repayments) proceeds from borrowings                                  (2,500)               3,601
                                                                            -------              -------
      Net cash provided by (used in) financing activities                    (2,500)               3,609

CASH PROVIDED BY DISCONTINUED OPERATIONS                                         --                1,115
                                                                            -------              -------

Increase (decrease) in cash and cash equivalents                                187               (2,082)
Cash and cash equivalents at beginning of period                                 --                3,312
                                                                            -------              -------

Cash and cash equivalents at end of period                                  $   187              $ 1,230
                                                                            =======              =======
</TABLE>


Supplemental disclosures of non-cash investing and financing activities:

         -        The Company received a $3.8 million note receivable from
                  Express-Med, Inc. in the sale of the Home Service Medical
                  business, to be paid over 42 months through March 1, 2004. The
                  Company has recorded the note on its September 29, 2000
                  balance sheet, offset by the deferred gain of the same amount.

See notes to consolidated financial statements


                                       5
<PAGE>   7

                                 CHRONIMED INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                   (UNAUDITED)

NOTE A--BASIS OF PRESENTATION

The accompanying unaudited condensed consolidated financial statements have been
prepared in accordance with generally accepted accounting principles for interim
financial information and with the instructions to Form 10-Q and Rule 10-01 of
Regulation S-X. Accordingly, they do not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements. In the opinion of management, all adjustments (consisting
of normal recurring accruals) considered necessary for a fair presentation have
been included. Operating results for the quarter ended September 29, 2000 are
not necessarily indicative of the results that may be expected for the year
ending June 29, 2001. For further information, refer to the financial statements
and footnotes thereto for the year ended June 30, 2000.

The balance sheet at June 30, 2000 has been derived from the audited financial
statements at that date, but does not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements.

The Company uses a four-week, four-week, five-week (4-4-5) quarterly accounting
cycle with the fiscal year ending on the Friday closest to June 30 and the
fiscal quarters ending on the Friday closest to the last day of the respective
month.

The Company intends to divest the Diagnostic Products business operated by its
wholly-owned subsidiary, MEDgenesis Inc., through a tax-free dividend to
shareholders or a sale of the business. The Company continues to engage in
negotiations to sell MEDgenesis while continuing to pursue the spin-off. As of
the date of this Form 10-Q, the Securities and Exchange Commission has not yet
approved the MEDgenesis Form 10 which is needed before the spin-off of
MEDgenesis can occur and the Company has not reached a definitive agreement
regarding the sale of the business. Until MEDgenesis is spun off or sold,
Chronimed must classify MEDgenesis as "discontinued operations" for financial
reporting purposes. As a result, all financial results concerning MEDgenesis
Inc., other than those classified as discontinued operations, have been removed
from this Form 10-Q leaving only the continuing operations of Chronimed Inc.

NOTE B--INVENTORIES

Inventories consist primarily of goods held for resale and are carried at the
lower of cost or market determined under the average cost method.



                                       6
<PAGE>   8
NOTE C--PER SHARE DATA

Earnings per share are calculated in accordance with SFAS No. 128, "Earnings Per
Share." Potential common shares are included in the diluted net income (loss)
calculation when dilutive. Potential common shares consisting of common stock
issuable upon exercise of outstanding common stock options are computed using
the treasury stock method. The Company's net income (loss) per share calculation
for basic and diluted is based on the weighted common shares outstanding. There
are no reconciling items in the numerator or denominator of the Company's net
income (loss) per share calculation. Employee stock options have been excluded
from the net income (loss) per share calculation because their effect would be
anti-dilutive or immaterial.

NOTE D--BUSINESS SEGMENT INFORMATION

The Company has two reportable segments. The Mail Order segment includes the
results of the Company's Biotech Injectables, Organ Transplant, and Home Service
Medical businesses. The Home Service Medical business was sold to Express-Med,
Inc. on September 1, 2000. The Retail segment includes the Company's HIV/AIDS
StatScript Pharmacy, as well as the Clinical Partners' Strategic Services line
and the Clinical Partners' case management line which was written off in the
quarter ended October 1, 1999. The table below presents information by
reportable segment.

<TABLE>
<CAPTION>

                                                  Mail Order            Retail               Total
                                                  ----------            ------               -----
<S>                                              <C>                 <C>                 <C>
         For the Quarter Ended 9/29/2000
               Revenue                             $ 34,839            $ 28,005            $ 62,844
               Loss from Operations                    (556)             (1,094)             (1,650)
         For the Quarter Ended 10/01/1999
               Revenue                             $ 26,833            $ 23,218            $ 50,051
               Loss from Operations                    (160)               (171)               (331)
</TABLE>

The difference between segment totals and the Company's consolidated totals
consist of corporate general and administrative expenses and other non-operating
items, both of which are not allocated to the segments. The following table is a
reconciliation of reportable segment income to the Company's consolidated
totals.

<TABLE>
<CAPTION>

                                                     Q1 FY2001        Q1 FY2000
                                                     ---------        ---------
<S>                                                <C>              <C>
             Total Consolidated Revenue:             $ 62,844         $ 50,051
                                                     ========         ========
             Loss from Operations:
             Total for reportable segments           $ (1,650)        $   (331)
             Unallocated amounts:
             --        Corporate G&A                      497             (650)
             --        Interest income                     50                7
             --        Interest (expense)                 (48)             (30)
             --        Other income (expense)              21               --
                                                     --------         --------
             Loss before income taxes                $ (1,130)        ($ 1,004)
                                                     ========         ========
</TABLE>



                                       7
<PAGE>   9
A change in segment assets occurred since June 30, 2000 with the sale of the
Home Service Medical business to Express-Med, Inc. on September 1, 2000. The
approximate net book value of the Home Service Medical business was $3.0 million
as of June 30, 2000. The assets of the Home Service Medical business are
included in the Mail Order segment. The following table presents assets by
reportable segment.

<TABLE>
<CAPTION>

                                    Mail Order             Retail        Corporate           Total
                                    ----------             ------        ---------           -----
<S>                              <C>                    <C>            <C>                <C>
As of 9/29/2000
      Segment Assets                 $29,772              $27,385          $ 7,000          $64,157

As of 6/30/2000
      Segment Assets                 $33,575              $27,818          $ 6,572          $67,965
</TABLE>

NOTE E--DISCONTINUED OPERATIONS

The Company intends to divest the Diagnostic Products business operated by its
wholly-owned subsidiary, MEDgenesis, Inc., through a tax-free dividend to
shareholders or a sale of the business. The Company continues to engage in
negotiations to sell MEDgenesis while continuing to pursue the spin-off. As of
the date of this Form 10-Q, the Securities and Exchange Commission has not yet
approved the MEDgenesis Form 10 which is needed before the spin-off of
MEDgenesis can occur and the Company has not reached a definitive agreement
regarding the sale of the business. Until MEDgenesis is spun off or sold,
Chronimed must classify MEDgenesis as "discontinued operations" for financial
reporting purposes. As a result, all financial results concerning MEDgenesis
Inc., other than those classified as discontinued operations, have been removed
from this Form 10-Q leaving only the continuing operations of Chronimed Inc.

On September 1, 2000, MEDgenesis paid a license transfer fee of $475,000 to
Hypoguard Limited, a UK-based medical device company. The license transfer fee
allowed MEDgenesis to continue selling certain diabetes strips upon completion
of the proposed spin off or sale based on technology developed by a subsidiary
of Medisys PLC. The license transfer fee has been included in the results of
discontinued operations. The license transfer fee was paid in consideration of
Hypoguard's consent to Chronimed's assignment of a technology license to
MEDgenesis, as necessitated by the spin-off or sale of MEDgenesis.

The discontinued operations represented by MEDgenesis contributed net income
after tax of $464,000 or four cents per share in the first quarter. This
compares to net income after tax of $436,000 or four cents per share in last
year's first quarter. Revenue for MEDgenesis was $9.1 million, up 12 percent
from last year's first quarter of $8.1 million.

NOTE F--SALE OF HOME SERVICE MEDICAL BUSINESS

Chronimed sold its Home Service Medical ("HSM") subsidiary on September 1, 2000
to Express-Med, Inc. of New Albany, Ohio for $6.5 million. HSM is a direct to
consumer, mail-order catalog business that contributed $14.9 million in revenue
to Chronimed's total results for the fiscal year ended June 30, 2000. The
Company received $3 million in cash and a $3.8 million subordinated note
maturing in 42 months and bearing an annual interest rate of 11%. In addition,
Chronimed will pay the buyer $282,000 on December 1, 2000 based on the
difference


                                       8
<PAGE>   10

between the net value of the purchased assets on Chronimed's balance sheet at
June 30, 2000 and September 1, 2000.

Chronimed deferred the $3.8 million gain on the sale of HSM in accordance with
the SEC Staff Accounting Bulletin No. 81, "Gain Recognition on the Sale of a
Business or Operating Assets to a Highly Leveraged Entity." The gain will be
deferred until principal payments under the promissory note are received. The
Company recorded the $3.8 million deferred gain on the balance sheet as a
deduction to notes receivable.

Based on the terms of the HSM asset purchase agreement, Express-Med, Inc. will
pay quarterly installments of accrued interest beginning March 1, 2001, and
annual $1 million installments of principal beginning September 1, 2001. The
entire outstanding balance of principal and interest becomes due on March 1,
2004. Given that there is no guarantee that Express-Med will be able to repay
the note and the long-term nature of the note, as stated above, Chronimed will
defer recognition of the gain on its income statement until the cash is
collected or deemed to be fully collectible. Chronimed believes that
Express-Med, Inc. will be able to fund the interest payments and therefore, the
Company will accrue the interest receivable monthly as earned.

NOTE G--SIGNIFICANT CONCENTRATIONS

Within the Mail Order segment, a major payor with whom Chronimed has a contract
(represented as two major payors merging into one during calendar year 1999)
represented 33% of the Company's revenue in the first quarter of fiscal 2001 and
25% in the first quarter of fiscal 2000.

NOTE H--FINANCIAL RESTATEMENT

The Company's financial statements for the fiscal year ended June 30, 2000 and
for the first three quarters of the fiscal year ended June 29, 2001 have been
restated. The restatement reflects a reduction in revenues, an increase in bad
debt expense, and an increase in allowance for doubtful accounts. These
adjustments are limited to the Company's Retail segment. The changes to the
financial statements resulting from the restatement are described below.

CONTINUING OPERATIONS

     REVENUE

     In the fourth quarter of fiscal 2001, management determined that software
     system and process errors in its Retail segment resulted in the
     overstatement of revenue. Following the implementation of new software
     systems in early fiscal 2000, certain transactions that had been canceled
     or rejected at the pharmacy level were transferred from the pharmacy
     operating system, without adjustment, to the Retail revenue accounting
     system, effectively resulting in a duplicate revenue entry. As a result,
     revenue was overstated in the Company's accounting records. The
     overstatement of revenue caused by these errors totaled $3,390,000 in
     fiscal 2000 ($827,000, $914,000, $979,000 and $670,000 for the first,
     second, third and fourth quarters, respectively) and $2,595,000 in fiscal
     2001 ($815,000, $1,030,000 and $750,000 for


                                       9
<PAGE>   11

     the first, second and third quarters, respectively). The Company has taken
     steps to correct its systems and processes to prevent duplicate revenue
     entries.

     In addition, management identified a large uncontracted payor in the
     Company's Retail segment that began paying claims in fiscal 2001 using a
     significantly lower rate schedule than the payor had previously used. As a
     result, the Company's traditional methods of estimating the revenue
     allowance for payor discounts did not accurately account for the
     significant reduction in reimbursement. The resulting overstatement of
     revenue in the first three fiscal quarters of fiscal 2001 totaled
     $1,918,000 ($760,000, $556,000 and $602,000 for the first, second and third
     quarters, respectively). The Company has taken steps to correct its systems
     and processes and to improve its methods for determining the revenue
     allowance for payor discounts.

     BAD DEBT EXPENSE AND ALLOWANCE FOR DOUBTFUL ACCOUNTS

     During fiscal 2001, management learned that personnel at the Company's
     Retail segment had fallen behind in posting cash receipts to customer
     accounts receivable records and were preparing aging reports that
     contained significant inaccuracies, which prevented timely and accurate
     monitoring of accounts receivable. Management determined that these
     inaccurate aging reports they had relied upon to estimate the allowance for
     doubtful accounts receivable at June 30, 2000 and the first three quarters
     of fiscal 2001 had caused them to underestimate the amount of the allowance
     at those dates. As a result, management has reassessed its estimate for
     doubtful accounts receivable and increased the allowance at June 30, 2000
     and at the end of each of the first three quarters of fiscal 2001. The
     allowance for doubtful accounts and the related bad debt expense was
     increased by $4,200,000 at June 30, 2000, and $989,000, $603,000 and
     $902,000 at the end of each of the first, second and third quarters,
     respectively, of fiscal 2001. The Company has taken steps to ensure the
     accuracy of the information on which it will base future estimates of
     doubtful accounts.

As a result, the fiscal 2000 financial statements, the 2000 and 2001 quarterly
results of operations, and related disclosures included in this Quarterly Report
have been restated to reflect the restatement of revenue, bad debt expense, and
accounts receivable. The effect of restatement on the quarters ended October 1,
1999 and September 29, 2000 is shown in the table below:

<TABLE>
<CAPTION>

                                                                              QUARTER ENDED
                                                                    ---------------------------------
                                                                    SEPTEMBER 29,          OCTOBER 1,
                                                                         2000                 1999
                                                                    -------------          ----------
<S>                                                                <C>                  <C>
     Net income (loss) from continuing operations,                      $ 861                $(108)
      as previously reported
     Impact of restatement for:
       Correction of Revenue Overstatement                               (961)                (504)
       Allowance for Doubtful Accounts                                   (604)                  --
                                                                        -----                -----
     Net (loss) from continuing operations,
       as restated                                                      $(704)               $(612)
                                                                        =====                =====
</TABLE>


                                       10
<PAGE>   12

As a result of the foregoing accounting adjustments, the Company's fiscal 2000
and 2001 condensed consolidated financial statements have been restated from the
amounts previously reported. The principal effects of these adjustments on the
accompanying financial statements are set forth below:

<TABLE>
<CAPTION>

                                                              QUARTER ENDED                     QUARTER ENDED
                                                            SEPTEMBER 29, 2000                 OCTOBER 1, 1999
                                                     --------------------------------    -------------------------------
                                                     AS PREVIOUSLY                       AS PREVIOUSLY
                                                        REPORTED        AS RESTATED         REPORTED        AS RESTATED
                                                     -------------    ---------------    -------------    --------------
<S>                                                <C>               <C>               <C>               <C>
Revenue                                                $ 64,419          $ 62,844          $ 50,878          $ 50,051
Gross profit                                              9,723             8,148             8,915             8,088
Income (loss) before income taxes                         1,434            (1,130)             (177)           (1,004)
Income tax (expense) benefit                               (573)              426                69               392
Net income (loss) from continuing
 operations                                            $    861          $   (704)         $   (108)         $   (612)
Net income (loss)                                      $  1,325          $   (240)         $    328          $   (176)
Basic and Diluted Earnings per Share:
 Net income (loss) from continuing operations          $   0.07          $  (0.06)         $  (0.01)         $  (0.05)
 Net income (loss)                                     $   0.07          $  (0.06)         $  (0.01)         $  (0.05)
</TABLE>

<TABLE>
<CAPTION>

                                                        AS OF SEPTEMBER 29, 2000               AS OF JUNE 30, 2000
                                                     --------------------------------    -------------------------------
                                                     AS PREVIOUSLY                       AS PREVIOUSLY
                                                        REPORTED        AS RESTATED        REPORTED         AS RESTATED
                                                     -------------    ---------------    -------------    --------------
<S>                                                <C>               <C>               <C>               <C>
Accounts receivable, net                               $ 45,890          $ 35,736          $ 47,352          $ 39,762
Total assets                                             80,906            74,711            83,060            78,430
Retained earnings                                        15,596             9,401            14,271             9,641
Total shareholders' equity                               68,635            62,440            67,687            63,057
</TABLE>




                                       11
<PAGE>   13

Part I.    Financial Information
Item 2.    MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
           CONDITION AND RESULTS OF OPERATIONS

OVERVIEW

         Chronimed Inc. ("Chronimed" or the "Company") is a disease-focused
company excelling in specialty pharmacy distribution for people with chronic
health conditions. The Company distributes pharmaceuticals and provides
specialized patient management services nationwide for people with long-term
chronic conditions such as organ transplants, HIV/AIDS, and diseases treated
with biotech injectable medications. Chronimed works directly with patients,
providers, insurance companies, health maintenance organizations, preferred
provider organizations, government agencies and other third party payors
("payors") to improve clinical and cost-of-care outcomes. The Company was
founded in 1985 as a Minnesota corporation and has been publicly traded on
Nasdaq since 1992.

         The Company distributes its pharmaceuticals and ancillary products by
mail and through its StatScript retail pharmacy chain. The patient populations
for which the Company's services are most effective include persons who:

  -      Have illnesses that generally occur in less than one percent of the
         nation's population;

  -      Require high-cost, complex medications, the majority of which must be
         taken for the rest of the patient's life and are not always available
         through traditional retail pharmacies;

  -      Require treatment by healthcare specialists; and

  -      Require a significant amount of self-management and ongoing education
         (where patient compliance is critical for improving clinical and
         financial outcomes).

         By focusing on select chronic conditions, the Company is able to
improve the quality of care for those people affected by these uncommon
diseases. In addition, the expertise Chronimed has developed makes it a valuable
partner for institutions, foundations and healthcare providers working with
patients afflicted with these chronic conditions. Chronimed also believes the
payors that pay a large portion of related healthcare costs do business with
Chronimed as a result of the Company's ability to improve care while minimizing
overall expenditures. Finally, Chronimed has spent many years establishing
relationships with the developers and manufacturers of prescription drugs and
other products needed to manage chronic conditions. The Company currently works
directly with all of these constituents in a concerted effort to improve
clinical and cost-of-care outcomes - and enhance the quality of life for the
chronically ill.

         Chronimed provides patients with a convenient, competitively priced
source of prescription drugs, counseling support, and a variety of educational
materials to help patients achieve maximum control over their chronic
conditions. Often, the greater the effort a patient makes to stabilize or
control his or her disease, the lower the incidence of complications and the
better the patient's quality of life. The Company believes that by educating
patients and increasing patient compliance, as well as provider support and
intervention, clinical outcomes can be improved, and long-term costs of care
reduced.


                                       12
<PAGE>   14

         Chronimed obtains patients primarily through referrals from healthcare
providers, direct patient contacts, and contracts with insurers and managed care
organizations. According to Medical Economics (April 10, 2000), an estimated 90%
of privately insured workers in the United States were enrolled in some type of
managed care program during 1999, up from 52% in 1993.

         The specialty pharmacy industry was developed principally in response
to the demand from employers and payors for more effective control of patient
care and cost increases in certain unusual chronic illnesses. As employers
attempt to control their escalating healthcare costs, they seek out providers
who have adopted various specialized managed care techniques. The increasing
majority of patient referrals come from contracts with payors and the government
as a result of the increased role of managed care and the Company's experience
in managing specific patient groups.

         The Company has also developed relationships with treatment centers,
foundations and medical associations that specialize in the treatment or support
of patients with chronic conditions. These relationships provide the Company
with access to a large number of individuals with chronic conditions and to the
healthcare specialists treating these conditions.

         Chronimed believes that its business model is well suited to support
developers and manufacturers of pharmaceutical products who are targeting small
or hard-to-identify patient populations. Chronimed provides these companies with
assistance in the rapid introduction of their products, a cost-effective means
for distributing these medications to specific patient populations, and a method
for monitoring product use and compliance.

RESTATEMENT

         The Company's financial statements for the fiscal year ended June 30,
2000 and for the first three quarters of the fiscal year ended June 29, 2001
have been restated. The restatement reflects a reduction in revenues, an
increase in bad debt expense, and an increase in allowance for doubtful
accounts. These adjustments are limited to the Company's Retail segment. See
Note H to the Company's Condensed Consolidated Financial Statements.

DISCONTINUED OPERATIONS

         On October 10, 2000 Chronimed announced that it was engaged in
negotiations to sell its MEDgenesis subsidiary while continuing to pursue a
spin-off of the business. No definitive agreement to sell MEDgenesis has been
reached and there can be no assurance that an agreement acceptable to Chronimed
will be negotiated. The Diagnostic Business has been operated by Chronimed's
wholly-owned subsidiary, MEDgenesis Inc., since July 1, 2000. MEDgenesis has
filed a Form 10 registration statement with the SEC to register MEDgenesis'
common stock under the Securities Exchange Act of 1934. The SEC must approve
this registration statement before a spin-off of MEDgenesis to Chronimed's
shareholders can take place. Chronimed and MEDgenesis are awaiting SEC approval
of the MEDgenesis Form 10 as of the date of this Form 10-Q. Until MEDgenesis is
spun off or sold, Chronimed must classify MEDgenesis as "discontinued


                                       13
<PAGE>   15

operations" for financial reporting purposes. Following the sale or spin-off of
MEDgenesis, Chronimed and MEDgenesis will no longer prepare or file consolidated
financial statements and tax returns. The two companies began independent
accounting as of July 1, 2000.

CONTINUING OPERATIONS

REVENUE

         Chronimed implemented the disclosure requirements of Financial
Accounting Statement No. 131, "Segment Reporting," in fiscal 1999. Chronimed is
comprised of two operating segments, Mail Order and Retail, based on the
business and how it is managed and resourced. The Mail Order segment currently
includes the Biotech Injectables program and Organ Transplant Pharmacy, and
prior to September 1, 2000, also included Home Service Medical (HSM). Chronimed
sold the Home Service Medical business on September 1, 2000. See Note F of Notes
to Condensed Consolidated Statements. The Retail segment includes the Company's
HIV/AIDS StatScript Pharmacy, as well as the Clinical Partners' Strategic
Services line and the Clinical Partners' case management line that was written
off in the quarter ended October 1, 1999.

      Total revenue increased 26%, from $50.1 million to $62.8 million, for the
first quarter ended October 1, 1999 and September 29, 2000 respectively. Price
increases and inflationary pressures have not been significant reasons for these
revenue increases. The contribution each segment made to total revenue is
discussed below.

      Mail Order segment revenue grew $8.0 million and 30% over last year's
first quarter, from $26.8 million to $34.8 million. The Biotech Injectables
business had significant new patient intakes from the Aetna U.S. Healthcare
contract, which became effective July 15, 2000, that created the increase in
revenue. Also, HSM was sold during the first quarter, resulting in reduced first
quarter revenue of $1.2 million, from $3.4 million last year compared to $2.2
million this year.

      Retail segment revenue grew $4.8 million and 21% over last year's first
quarter, from $23.2 million to $28.0 million. This growth came from the
StatScript Pharmacy, which grew $5.1 million and 23% in revenue over last year's
first quarter. Existing stores contributed 79% of the growth compared to 21%
from new stores. The Company slowed new store growth due to its focus on
exploring strategic initiatives and the MEDgenesis spin-off in the prior year.
StatScript's growth was partially offset by a $300,000 decline over last year's
first quarter revenue due to the fiscal 2000 exit from the Clinical Partners
case management line.

      Overall revenue growth for fiscal 2001 is expected to be about 25 to 30
percent over fiscal 2000 and is expected to continue in both Chronimed's
operating segments. The Company expects revenue for the year to be approximately
$270 million. This would represent 28 percent revenue growth in fiscal 2001
against an adjusted fiscal 2000 revenue stream of $211 million (both years
having been adjusted for the September 2000 sale of the Home Service Medical
business). The Company's ability to maintain and add contracts in its Mail Order
business is important to this projection. The Company's expectation to open four
or more stores this year, resulting in at least


                                       14
<PAGE>   16

36 stores by fiscal 2001 year-end, is also important to this projection. The
Company believes that its supplier inputs and pharmacy fulfillment rates are
stable and sustainable but may be subject to unforeseen shortfalls. The Company
cautions readers that this and other paragraphs in the Management's Discussion
section include "forward-looking statements" within the meaning of the Private
Securities Litigation Reform Act of 1995 and that actual results may differ
materially from projections. Readers should review the Outlook section in this
Form 10-Q for further information.

GROSS PROFIT

      Gross profit dollars showed almost no growth, at approximately $8.1
million each year. First quarter gross profit percentage decreased from 16.2%
last year to 13.0% this year. The sale of the HSM business, which reduced margin
dollars from $1.0 million in the first quarter of fiscal 2000 to $500,000 in the
first quarter of fiscal 2001, partially offset the Company's increase in margin
dollars. The decrease in gross profit percentage was due partly to reduced
margins in the mail order business caused by managed care pricing pressure
within the Biotech Injectables business. The gross profit percentage also
decreased slightly due to the sale of HSM and its higher gross profit percentage
relative to the rest of the mail order business. In addition, the Retail segment
faced continuing reimbursement pressures resulting in significantly reduced
gross profit percentages. Managed care pricing pressure is expected to continue
both in the mail order and retail businesses.

SELLING AND MARKETING EXPENSES

      Overall selling and marketing expenses in the first quarter were down
approximately $90,000 and 7% compared to last year's first quarter, on overall
revenue growth of 26%. The Home Service Medical sale in first quarter fiscal
2001 and the discontinuance of the Clinical Partners contract/case management
line in third quarter fiscal 2000 resulted in a $200,000 decrease in selling and
marketing expenses compared to last year's first quarter. This decrease was
partially offset by expanded selling efforts in the Company's Organ Transplant
business in the Mail Order segment. Organ Transplant spending increased $95,000
in the first quarter of fiscal 2001 versus last year's first quarter. As a
percentage of revenue, selling and marketing expenses dropped from 2.4% in last
year's first quarter to 1.8% in this year's first quarter.


                                       15
<PAGE>   17

GENERAL AND ADMINISTRATIVE AND BAD DEBT EXPENSES

      Combined general and administrative (G&A) and bad debt expenses for the
first quarter totaled $8.2 million, up 4% from $7.9 million last year. As a
percentage of revenue, these combined expenses decreased from 15.7% last year to
13.0% this year. There are a number of factors that contributed to the net
increase of approximately $300,000 in combined G&A and bad debt expenses. First,
Chronimed incurred $400,000 of costs related to the Company's pursuit of
strategic alternatives in the first quarter of fiscal 2000 and incurred no such
related costs in this year's first quarter. When Chronimed announced its
intention to spin off its Diagnostic Products business in the third quarter of
fiscal 2000, it also announced the discontinuance of its exploration of
strategic alternatives with an investment banker. Second, approximately $700,000
of G&A costs from the Clinical Partners case management line in the Retail
segment were incurred in last year's first quarter and no similar costs were
incurred in this year's first quarter. The Clinical Partners case management
line was written off and shut down in the third quarter of fiscal 2000. Third,
the Home Service Medical business within the Mail Order segment incurred
$100,000 less in G&A expenses during this year's first quarter compared to last
year's first quarter. Due to its sale September 1, 2000, the Home Service
Medical business operated as a business unit of Chronimed only two of the three
months in this year's first quarter. Fourth, bad debt expense increased
approximately $400,000 in first quarter of fiscal 2001, primarily resulting from
a $989,000 provision made as part of the Company's financial restatement and
reassessment of its allowance for doubtful accounts. Absolute dollars spent in
the first quarter increased significantly in the Biotech Injectables business of
the Mail Order segment and in the StatScript business of the Retail segment due
to an increase in variable expenses that have grown directly with 26% revenue
growth including StatScript pharmacies, customer service, billing and
fulfillment.

INTEREST INCOME

      Net interest income increased to $2,000 in this year's first quarter with
$50,000 of interest income and $48,000 of interest expense. In the first quarter
of fiscal 2000 net interest expense was $23,000. Interest income increased in
the first quarter of fiscal 2001 as a result of the $3.8 million note receivable
from the sale of the Home Service Medical business. Interest expense increased
from short-term borrowing to support a significantly higher revenue and asset
base.

INCOME TAXES

      The Company's income tax rate was approximately 38% in the first quarter
ended September 29, 2000 compared to 39% in the first quarter ended October 1,
1999.  The current first quarter rate of 38% is expected to continue or to be
slightly higher through fiscal 2001 year-end.


                                       16
<PAGE>   18

LIQUIDITY AND CAPITAL RESOURCES

      Net cash provided by operating activities was $253,000 during the first
quarter of fiscal 2001. Receivables decreased by $2.0 million, net of the sale
of HSM assets, due to improvements in accounts receivable days sales outstanding
(DSO's) occurring primarily in the Mail Order segment. The Injectables business
within the Mail Order segment is beginning to see timing and process
improvements in collections from its largest payor. Inventory decreased by
$470,000. Even though the Company experienced 8% sequential quarter revenue
growth, days on hand inventory improved from eleven days at June 30, 2000 to ten
days at September 29, 2000. The Company believes that it is properly reserved
for excess and obsolete inventory. Accounts payable and accrued expenses
decreased $716,000 due to timing of payments. Depreciation and amortization
totaled $871,000 and the tax receivable increased by $1,244,000 during the first
quarter of fiscal 2001.

      Net cash generated by investing activities was $2.4 million during the
first quarter of fiscal 2001. The Company received $3.0 million in proceeds from
the sale of the Home Service Medical business. Capital expenditures totaled
$566,000 and were for computer hardware and software, and leasehold improvements
for StatScript pharmacies.

      Net cash used in financing activities was $2.5 million used to pay the
balance on the line of credit. There was no balance outstanding under the line
of credit at September 29, 2000 and $2.5 million outstanding as of June 30,
2000.

      As of September 29, 2000 Chronimed had working capital of $36.2 million
compared to $36.4 million as of June 30, 2000. The Company expects working
capital requirements for accounts receivable and inventory to increase as
revenue increases. The Company's accounts receivable are generally with Payors
for which the collection periods vary depending on the practices of the
individual Payor and whether or not Chronimed has a contract with the Payor.
Electronic billing and on-line adjudication of claims are positive trends that
shorten cash collection periods and improve cash flow.

      The Company has a discretionary line of credit of $15 million. The Company
believes that the line of credit and cash provided by operating activities will
allow it to meet foreseeable cash requirements and provide the flexibility to
fund future growth. Any material business acquisitions would need to be financed
from debt or equity sources beyond the Company's line of credit and cash flow
from operations. The Company has no long-term debt. Shareholder's equity was
$62.4 million at the end of this year's first quarter and $63.1 million at
fiscal 2000 year-end.

GOVERNMENT REGULATION

         The Company's business is subject to substantial governmental
regulation including laws governing the dispensing of prescription drugs and
laws prohibiting the payment of remuneration for patient referrals. Because
sanctions may be imposed for violations of these laws, compliance is a
significant operational requirement for the Company. Management believes the
Company is in substantial compliance with all existing statutes and regulations
materially affecting the conduct of its business.


                                       17
<PAGE>   19

         Political, economic and regulatory influences are subjecting the
healthcare industry and prescription drug providers in the United States to
fundamental change. A variety of new approaches have been proposed, including
mandated basic healthcare benefits, controls on healthcare spending through
limitations on the growth of private health insurance premiums and Medicare and
Medicaid spending, and the creation of large purchasing groups. In addition,
some of the states in which the Company operates have adopted or are considering
various healthcare reform proposals. The Company anticipates that Congress and
state legislatures will continue to review and assess alternative healthcare
delivery systems and payment methods and that public debate of these issues will
likely continue in the future.

SEASONALITY

         The Company has experienced a significant seasonal pattern in its
operating results. Historically, the Company has had higher revenue in its
second fiscal quarter (ending December) than in its third fiscal quarter (ending
March). The Company believes the seasonality of its revenue and earnings comes
from the acceleration of purchases of prescription drugs and related medical
products by individuals with non-contracted indemnity insurance prior to the
beginning of a new calendar year (which is generally when payors impose new
deductible calculations). As the overall business grows, the Company expects the
seasonal pattern will soften and that third quarter revenue will be the same as
or higher than second quarter revenue. In addition, the sale of the Home Service
Medical business will diminish the effects of seasonality in the Mail Order
segment due to HSM's high degree of seasonality. In fiscal 2000, Home Service
Medical's revenue was $3.4 million in the first quarter, increased 55% to $5.3
million in the second quarter, and decreased 54% to $2.4 million in the third
quarter.

OUTLOOK

         Information contained in this "Management's Discussion and Analysis of
Financial Condition and Results of Operations", other than historical or current
facts, should be considered forward looking statements as defined in the Private
Securities Litigation Reform Act of 1995. These statements reflect management's
current views of future events and financial performance that involve a number
of risks and uncertainties. Chronimed undertakes no obligation to update any
such statements to reflect later developments. Factors that could cause actual
results to differ include, but are not limited to, the following: changes in
economic conditions; general competitive factors; pressures on gross profit
margins; the Company's ability to execute its sales and marketing plans; changes
in the status of managed care contracts, particularly but not limited to Aetna
U.S. Healthcare; changes in ownership; material litigation; the Company's
ability to complete the divestiture of its diagnostic products business via sale
or spin-off; and the risks described from time to time in the Company's public
reports filed with the SEC. Please see Exhibit 99 filed with the Company's Form
10-K on September 27, 2000 for additional circumstances that could cause actual
results to differ from forecasts. Investors are specifically referred to such
cautionary statements for discussion of factors that could affect the Company's
operations and forward-looking statements contained herein.


                                       18
<PAGE>   20

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

         Investments as of June 30, 2000 and September 29, 2000 are classified
as Available-for-Sale and consisted of equity securities of Cell Robotics
International, Inc., with whom the Company had a distribution and development
agreement for the Lasette laser lancing device. The Company considers any net
unrealized gain or loss on these investments to be temporary and reflects such
gains or losses as a component of shareholders' equity. The Cell Robotics
securities became the property of MEDgenesis Inc. effective July 1, 2000 in
association with the establishment of MEDgenesis as a wholly-owned subsidiary of
Chronimed and, accordingly, are included in net assets of discontinued
operations.





                                       19
<PAGE>   21
PART II.   OTHER INFORMATION


Items 1, 2, 3, 4 and 5 required under Part II have been omitted since they are
not applicable or the answers are negative.


Item 6.  Exhibits and Reports on Form 8-K

         a.)      Exhibits

                  None

         b.)      Reports on Form 8-K

                  None.



                                       20
<PAGE>   22
                                   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.


                                                   CHRONIMED INC.
                                                   --------------
                                                    (REGISTRANT)

October 11, 2001                         By    /s/ Henry F. Blissenbach
----------------                              -------------------------
     Date                                     Henry F. Blissenbach
                                              Chief Executive Officer and
                                              Chairman of the Board of Directors


October 11, 2001                              /s/ Gregory H. Keane
----------------                         -------------------------
     Date                                         Gregory H. Keane
                                         Vice President, Chief Financial Officer