<PAGE>

  =============================================================================
                    U.S. SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

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

                                  FORM 10-Q/A
                                Amendment No. 1

 [X] QUARTERLY REPORT UNDER SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE
                                  ACT OF 1934
                 For the quarterly period ended June 30, 2000

                                      or

 [_] TRANSITION REPORT UNDER SECTION 13 OR 15 (d) OF THE EXCHANGE ACT OF 1934
                       For the transition period from   to

                                 _____________


                        Commission file number 0-27914

                        RIBOZYME PHARMACEUTICALS, INC.
            (Exact name of registrant as specified in its charter)

                                  _____________

            Delaware                                  34-1697351
            --------                                  ----------
   (State of incorporation)             (I.R.S. Employer Identification No.)

                             2950 Wilderness Place
                            Boulder, Colorado 80301
                   (Address of principal executive offices)

                  Registrant's telephone number: (303) 449-6500

                                  _____________


Check 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 ___
   -----

The number of shares of the registrant's common stock, par value $0.01 per
share, outstanding as of August 4, 2000 was 15,288,446.

We hereby amend Items 1 and 2 and Exhibit 27, of our Quarterly Report on Form
10-Q for the period ending June 30, 2000 to read in their entirety as set forth
below.
<PAGE>

                         RIBOZYME PHARMACEUTICALS, INC.
                               INDEX TO FORM 10-Q
<TABLE>
<CAPTION>
PART 1 - FINANCIAL INFORMATION                                                                             PAGE
                                                                                                           ----
<S>                                                                                                        <C>
Item 1.  Financial Statements

         Condensed Balance Sheets as of June 30, 2000 (unaudited) and
         December 31, 1999.................................................................................. 3

         Condensed Statements of Operations - Three and Six Months Ended
         June 30, 2000 and 1999 (unaudited)................................................................. 4

         Condensed Statements of Cash Flows - Six Months Ended

         June 30, 2000 and 1999 (unaudited)................................................................. 5

         Notes to Condensed 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.........................................13

PART II - OTHER INFORMATION

Item 2.  Changes in Securities.............................................................................. 13
Item 4.  Submission of Matters to a Vote of Security Holders................................................ 14
Item 6.  Exhibits and Reports on Form 8-K .................................................................. 15

SIGNATURES.................................................................................................. 16

Exhibit Index............................................................................................... 17
</TABLE>
                                       2
<PAGE>

PART I. FINANCIAL INFORMATION
ITEM I. FINANCIAL STATEMENTS

                         RIBOZYME PHARMACEUTICALS, INC.
                            CONDENSED BALANCE SHEETS

<TABLE>
<CAPTION>
                                     ASSETS
                                     ------
                                                              June 30,
                                                                2000               December 31,
                                                             (restated)                1999
                                                                ----                   ----
                                                             (unaudited)
<S>                                                       <C>                     <C>
Current assets
   Cash and cash equivalents                              $  59,530,028          $   9,749,822
   Securities available-for-sale                              4,050,476              4,250,259
   Accounts receivable                                        1,697,681              1,545,164
   Accounts receivable-related parties                        2,096,000                484,729
   Prepaid expenses and other current assets                    480,312                256,571
                                                          -------------          -------------
Total current assets                                         67,854,497             16,286,545

Property, plant and equipment at cost,
   net of accumulated depreciation                            3,317,976              3,803,906

Notes receivable-related parties                                234,284                313,750
Deferred patent costs, net                                    4,342,277              4,231,307
Investment in Medizyme                                        8,431,141                      -
Other assets                                                    462,935                456,591
                                                          -------------          -------------

Total assets                                              $  84,643,110          $  25,092,099
                                                          =============          =============

                      LIABILITIES AND STOCKHOLDERS' EQUITY
                      ------------------------------------

Current liabilities
-------------------
   Accounts payable-trade                                 $     479,580          $     974,309
   Accrued liabilities                                          720,622                626,153
   Deferred revenue, current portion-related parties            400,000                400,000
   Current portion of long-term debt                             74,863                200,455
                                                          -------------          -------------
Total current liabilities                                     1,675,065              2,200,917

Deferred revenue, long-term portion-related parties           1,000,004              1,200,001
Convertible debt-related parties                                      -              6,810,537

Stockholders' equity
--------------------
   Preferred stock                                                  120                      -
   Preferred stock issuable                                     360,450                      -
   Common stock                                                 152,851                112,633
   Additional paid-in capital                               171,226,201             98,894,100
   Deferred compensation and other                              (41,718)               (43,017)
   Accumulated deficit                                      (89,729,863)           (84,083,072)
                                                          -------------          -------------
Total stockholders' equity                                   81,968,041             14,880,644
                                                          -------------          -------------

Total liabilities and stockholders' equity                $  84,643,110          $  25,092,099
                                                          =============          =============
</TABLE>

See notes to condensed financial statements

                                       3
<PAGE>

                        RIBOZYME PHARMACEUTICALS, INC.
                      CONDENSED STATEMENTS OF OPERATIONS
                                  (Unaudited)

<TABLE>
<CAPTION>
                                                           Three months ended                  Six months ended
                                                                June 30,                          June 30,
                                                               (restated)                        (restated)
                                                    ------------------------------      ----------------------------
                                                         2000             1999              2000             1999
                                                         ----             ----              ----             ----
<S>                                                 <C>               <C>               <C>             <C>
Revenue
   Collaborative agreements                         $  2,666,037      $  1,747,589      $  5,205,608    $  2,856,181
   Collaborative agreements-related parties            1,214,932           428,149         2,545,227       1,020,792
                                                    ------------      ------------      ------------    ------------
Total revenues                                         3,880,969         2,175,738         7,750,835       3,876,973

Expenses
   Research and development                            3,922,072         3,624,690         8,786,907       7,385,123
   General and administrative                          1,058,306           537,038         2,097,176       1,096,334
                                                    ------------      ------------      ------------    ------------
Total expenses                                         4,980,378         4,161,728        10,884,083       8,481,457

Operating loss                                        (1,099,409)       (1,985,990)       (3,133,248)     (4,604,484)
Other income (expense)
   Interest income                                       913,735           112,720         1,161,424         202,935
   Interest expense                                       46,931          (149,217)          (91,108)       (261,308)
   Equity in loss of
       unconsolidated affiliate                       (1,786,033)         (203,701)       (3,583,859)       (698,325)
                                                    ------------      ------------      ------------    ------------
   Total other income (expense)                         (825,367)         (240,198)       (2,513,543)       (756,698)

Net loss                                            $ (1,924,776)     $ (2,226,188)     $ (5,646,791)   $ (5,361,182)
                                                    ============      ============      ============    ============

Net loss per share (basic and diluted)              $      (0.13)     $      (0.24)     $      (0.42)   $      (0.58)

Shares used in computing net loss per share           15,009,834         9,213,717        13,442,457       9,197,993
                                                    ============      ============      ============    ============
</TABLE>

See notes to condensed financial statements

                                       4
<PAGE>

                        RIBOZYME PHARMACEUTICALS, INC.
                      CONDENSED STATEMENTS OF CASH FLOWS
                                  (Unaudited)

<TABLE>
<CAPTION>
                                                                         Six months ended
                                                                              June 30,
                                                                   -----------------------------
                                                                       2000
                                                                    (restated)          1999
                                                                       ----             ----
<S>                                                                <C>              <C>
Operating Activities
Net loss                                                            $ (5,646,791)    $ (5,361,182)
   Adjustments to reconcile net loss to
      net cash used in operating activities:
   Depreciation and amortization                                         873,198          817,263
   Equity in loss of unconsolidated affiliate                          3,583,859          698,325
   Compensation for forgiveness of notes
      receivable-related parties                                          79,466           67,466
   Compensation related common stock and options                       1,351,138           25,620
   Expense related to warrant repricing                                        -           42,221
   Accrued interest included in convertible debt                          86,667          207,063
   Changes in operating assets and liabilities:
      Accounts receivable                                             (1,763,788)       1,304,644
      Prepaid expenses and other                                        (223,741)        (304,467)
      Other assets                                                        (6,344)           3,925
      Accounts payable                                                  (494,729)        (118,150)
      Accrued expenses                                                    94,469          (42,615)
      Deferred license revenue                                          (199,997)        (200,000)
                                                                    ------------     ------------
   Net cash used in operating activities                              (2,266,593)      (2,859,887)

Investing activities

   Additions to property, plant and equipment                           (324,140)        (608,174)
   Additions to deferred patent costs                                   (174,099)        (150,757)
   Net sales (purchases) of securities available-for-sale                201,081       (1,000,000)
   Investment in unconsolidated affiliate                            (12,015,000)               -
   Loan advances-related parties                                               -          (97,187)
                                                                    ------------     ------------
   Net cash used in investing activities                             (12,312,158)      (1,856,118)

Financing activities

   Net proceeds from sale of common and preferred stock               70,384,548        7,664,942
   Payments under loan facilities                                     (7,025,591)        (195,840)
   Borrowings under loan facilities                                    1,000,000        2,000,000
                                                                    ------------     ------------
   Net cash provided by financing activities                          64,358,957        9,469,102

Net increase in cash and cash equivalents                             49,780,206        4,753,097
Cash and cash equivalents at beginning of period                       9,749,822        6,511,512
                                                                    ------------     ------------
Cash and cash equivalents at end of period                          $ 59,530,028     $ 11,264,609
                                                                    ============     ============
</TABLE>

See notes to condensed financial statements.

                                       5
<PAGE>

                        RIBOZYME PHARMACEUTICALS, INC.
                    NOTES TO CONDENSED FINANCIAL STATEMENTS
                                 June 30, 2000
                                  (Unaudited)

Note 1: Basis of Presentation

     The accompanying unaudited condensed 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 Article 10 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 three and six-month period ending June
30, 2000 are not necessarily indicative of the results that may be expected for
the year ended December 31, 2000. For further information, refer to the
financial statements and footnotes thereto included in our annual report on Form
10-K for the year ended December 31, 1999.

     Certain amounts in the 1999 financial statements have been reclassified in
order to conform with the 2000 presentation.

Note 2: Public Offering

     In April 2000, we completed a public offering of 3,150,000 shares of our
common stock that resulted in gross proceeds of $56.7 million. After underwriter
fees and expenses are deducted, net proceeds are expected to be approximately
$52.7 million. In April 2000 we repaid $6.9 million of our outstanding
borrowings from Schering AG with proceeds from this offering.


Note 3: Restatement

The Company has previously accounted for its Employee Stock Purchase Plan (the
Purchase Plan) as compensatory for financial reporting purposes. However, the
Purchase Plan does qualify for non compensatory treatment under Section 423 of
the Internal Revenue Code. During the third quarter of 2000, the Company's
management determined that its policy was not in compliance with existing
authoritative guidance as promulgated under Accounting Principles Board
Statement No. 25, Accounting for Stock Issued to Employees (APB 25) and the
recently issued Financial Accounting Standards Board Interpretation No. 44,
Accounting for Certain Transactions Involving Stock Compensation -- an
Interpretation of APB 25 (FIN 44). As a result, the Company's quarterly
financial statements as of and for the three and six month periods ended June
30, 2000 have been restated to comply with this guidance. The effect of the
restatement resulted in a reduction of recorded stock compensation expense of
$628,000 for the three and six month periods ending June 30, 2000. The effect
of the Company's previous accounting treatment on periods prior to the June 30,
2000 quarter is immaterial, and thus, these periods have not been restated.

The accompanying balance sheet, statement of operations, and statement of cash
flows have been restated to reflect these adjustments. The following summarizes
key financial statement items that were affected by the restatement (all amounts
in thousands):
<TABLE>
<CAPTION>

                                             As Originally        As
                                               Reported         Restated
                                            ------------------------------
<S>                                         <C>               <C>
As of June 30, 2000
Stockholders' equity:
Additional paid-in capital                  $        171,854    $  171,226
Accumulated deficit                                  (90,358)      (89,730)
Other stockholders' equity                               472           472
                                            ------------------------------
Total stockholders' equity                  $         81,968    $   81,968
                                            ==============================

For the three months ended June 30, 2000
Research and development expenses           $          4,376    $    3,922
General and administrative expenses         $          1,232    $    1,058
Net loss                                    $         (2,553)   $   (1,925)
Net loss per share (basic and diluted)      $          (0.17)   $    (0.13)

For the six months ended June 30, 2000
Research and development expenses           $          9,241    $    8,787
General and administrative expenses         $          2,271    $    2,097
Net loss                                    $         (6,275)   $   (5,647)
Net loss per share (basic and diluted)      $          (0.47)   $    (0.42)

</TABLE>

                                       6
<PAGE>

ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
        OF OPERATIONS.

Forward-looking Statements

     Statements in this Form 10-Q/A, which are not strictly historical, are
"forward-looking" statements which should be considered as subject to the many
uncertainties that exist in our operations and business environment. These
uncertainties, which include, among other things, the following: general
economic and business conditions; competition; technological advances; ability
to obtain rights to technology; ability to obtain and enforce patents; ability
to commercialize and manufacture products; ability to obtain collaborators;
ability to manufacture ribozymes in adequate amounts for its collaborations and
clinical trials; results of clinical studies; results of research and
development activities; business abilities and judgment of personnel;
availability of qualified personnel; changes in, or failure to comply with,
governmental regulations; ability to obtain adequate financing in the future;
and the like, are set forth in our 10-K for the year ended December 31, 1999
which is on file with the U.S. Securities and Exchange Commission, a copy of
which is available from us.

Overview of our Business

     We are developing a new class of drugs based on engineered molecules called
"ribozymes." Ribozymes are a form of ribonucleic acid that have the ability to
cleave RNA, including mRNA, and thereby selectively inhibit protein production.
Because many human diseases result from abnormal protein production, we believe
that ribozymes are applicable to a broad range of human diseases. We are
currently in clinical development and preclinical testing for three product
candidates and expect to begin preclinical testing on one additional product
candidate by the end of 2000.

     We are conducting a Phase I/II clinical trial for our lead product
candidate, ANGIOZYME(TM), for the treatment of solid tumor cancers in
collaboration with Chiron Corporation and expect to complete this trial before
the end of 2000. Also, Phase I/II clinical trials for our anti-HCV ribozyme for
the treatment of Hepatitis C have been initiated with Eli Lilly and Company. The
current clinical trials in these programs will be completed in the fourth
quarter of 2000 and the results could significantly and materially impact our
business, operations and ability to raise additional capital.

     In January 2000, we announced completion of a joint venture with Elan
Corporation, Medizyme Pharmaceuticals, Ltd., whereby we have licensed
HERZYME(TM) and Elan has licensed its MEDIPAD(R) technology to the joint
venture. HERZYME (TM) is our potential product to treat breast and other
cancers. MEDIPAD(R) is a multi-day disposable continuous subcutaneous drug
delivery system that allows a patient to administer the drug at home. Initial
funding of Medizyme included $12.0 million from us and $3.0 million from Elan.
Currently, we own 80.1% of Medizyme's capital stock and Elan owns 19.9%. We have
estimated that funding for Medizyme will require approximately $15.0 million in
additional operating and development costs and, therefore, Elan has provided us
with a $12.0 million credit facility on a draw-down basis for us to use, if
desired, to fund our portion of Medizyme operating costs over a 30 month period.
The debt has a 12% rate and may ultimately be converted into our common stock at
a 50% premium to the average price of our common stock for the 60 trading days
prior to the time of the applicable draw down on the credit facility.

     To date, we have committed substantially all our resources to our research
and product development programs. We have not generated any revenues from
product sales, nor do we anticipate any in the foreseeable future. Revenue
recorded from our collaborative agreements consists of:

 .    Up front revenue. Up front revenue is fully recognized upon signing a
     collaboration and is related to the value of the research at that point in
     time. Up front revenue may also be a reimbursement to us of recent expenses
     which we incurred related to product development. All up front revenues
     recognized represents the culmination of a separate earnings process.

 .    Research revenue. Typically research revenue is based on the fully burdened
     cost of a researcher working on a collaboration. Rates are billed per
     employee, per year, prorated for time worked on a project. This revenue is
     typically invoiced on a quarterly basis, either up front or in arrears.
     Revenue is recognized ratably over the period, with the balance reflected
     as deferred revenue until earned. The revenue is typically recurring over
     the term of a collaboration.

 .    License revenue. License revenue is recognized ratably over the term of the
     license. Payments received in advance are recorded as deferred revenue
     until earned.

 .    Milestone revenue. Milestone revenue is recognized in full when the related
     milestone performance goal is achieved. Milestone revenue is typically not
     consistent or recurring in nature.

     Our revenue has consisted primarily of research revenue payments from our
collaborators. All revenues are either deferred as a liability or recognized
upon satisfying revenue criteria. As of June 30, 2000, all revenues that have
been recognized are earned and no further obligations exist for such

                                       7
<PAGE>

revenue. We depend upon funding from external financing and corporate
collaborations for our research and product development programs and expect to
do so for the foreseeable future.

     We have not been profitable since inception and have an accumulated deficit
of $89.7 million as of June 30, 2000. Losses have resulted primarily from our
research and development programs. We expect to incur additional losses as
ANGIOZYME(TM), the anti-HCV ribozyme, HERZYME(TM), and other product candidates
advance through development. In addition, future milestone payments under some
of our collaborations are contingent upon our meeting particular research or
development goals. The amount and timing of future milestone payments are
contingent upon the terms of each collaboration agreement. In some instances, we
may forfeit milestone payments if we fail to accomplish a goal within a certain
time frame. Therefore, we are subject to significant variation in the timing and
amount of our revenues and results of operations from period to period.

     In 1998, we transferred our target discovery and validation technology to
Atugen Biotechnology AG in exchange for a substantial equity interest. We will
continue our existing target discovery and validation agreements with our
collaborators by subcontracting services to be performed to Atugen. We currently
own 48.4% of Atugen and will record our share of any future profits. In 1999,
through the recognition in the losses of Atugen, we eliminated our remaining
investment in Atugen.

     Our revenues are denominated in U.S. dollars, therefore, we have not been
exposed to foreign currency translation risks and have not engaged in any
hedging instruments.

Results of Operations

Three and Six Months Ended June 30, 2000 and 1999

     Revenues. Generally, revenue fluctuations result from changes in the number
of funded research projects as well as the timing and completion of contract
milestones. Our revenues are split into two categories: (i) Collaborative
agreements and (ii) Collaborative agreements-related parties. Collaborative
agreement revenues currently includes revenues recorded from Chiron and Lilly.
Chiron revenues are related to our joint collaboration on ANGIOZYME(TM). Lilly
revenues relate to our collaboration on our anti-HCV ribozyme product for the
treatment of Hepatitis C. Collaborative agreements-related parties currently
includes revenues recorded from Medizyme and Atugen. Collectively, collaborative
revenues increased to $3.9 million and $7.8 million for the three and six months
ended June 30, 2000, from $2.2 million and $3.9 million for the corresponding
periods in 1999. The increase of $1.7 million for the quarter ending June 30,
2000 was primarily due to a $1.0 million milestone payment from Lilly received
in June 2000 as a result of meeting a clinical development milestone with the
anti-HCV ribozyme. Also, due to timing of expenses, Lilly revenues for the
quarter ending June 30, 2000 increased $255,000 over the same period last year.
In addition, we recorded $960,000 in revenues related to Medizyme, which in 1999
did not yet exist. Revenues from Chiron and Atugen for the quarter were down by
$296,000 and $172,000, respectively, compared to the same period last year.
Revenues from Chiron and Atugen are expected to fluctuate due to timing of
expenses and, in Atugen's case, scaling back of business development and
administrative services provided.

     The increase of $3.9 million for the six month period ending June 30, 2000
was primarily due to $1.9 million recorded from Medizyme, which did not exist in
1999 and incremental revenues of $2.4 million from Lilly recorded in 2000. The
2000 Lilly revenues include the $1.0 million milestone payment referenced above.
In addition, Lilly revenues in 2000 include two quarters of revenues, while in
1999 include only one quarter of revenues because the Lilly collaboration was
finalized in March 1999. Revenues recorded from Atugen have decreased to
$613,000 from $1.0 million for the six month period ending June 30, 2000 from
the same period ending in 1999. The decrease is due to a reduction of the


                                       8
<PAGE>

management and administrative services that we provide because Atugen no longer
requires the extensive services needed when it was first established in 1999.

     Expenses. Research and development expenses increased to $3.9 million and
$8.8 million for the three and six months ended June 30, 2000, compared to $3.6
million and $7.4 million for the corresponding periods in 1999. The increase was
due in part to approximately $261,000 and $209,000 of a non-cash, stock option
compensation expense recorded for performance stock options that vested during
the first and second quarters, respectively, in 2000. During the first and
second quarters, a number of research and development milestones were achieved,
including filing the IND and commencing Phase I for the anti-HCV ribozyme, as
well as starting pre-clinical development of HERZYME(TM). Accounting rules
require that the difference between the market price and an option grant price
must be expensed as compensation. During the first six months of 2000, our stock
price achieved considerable highs on dates when performance options vested,
resulting in significant non-cash stock compensation expense. In addition,
increased expenses for the first and second quarters of 2000 included
approximately $280,000 and $270,000 of expenses related to increased staffing.
The increase for the period ending June 30, 2000 from the same period in 1999
was also due to an increase of approximately $313,000 for clinical trial
expenses related to ANGIOZYME(TM) and research expenses relating to the anti-HCV
ribozyme. Other expenses have increased accordingly, due to increased staffing
and the expansion of our development programs. We expect research and
development expenses, including pre-clinical studies and clinical trials, to
continue to increase as we expand our development programs for ANGIOZYME(TM),
the anti-HCV ribozyme and HERZYME(TM).

     General and administrative expenses increased to $1.1 million and $2.1
million for the three and six months ended June 30, 2000, compared to $537,000
and $1.1 million for the corresponding periods in 1999. The increase was
primarily due to approximately $461,000 and $881,000 of non-cash, stock option
compensation expense recorded for performance stock options that vested during
the three and six month period ending June 30, 2000, respectively. During the
first and second quarters of 2000, a number of corporate milestones were
accomplished, including achieving a market capitalization of $150 million or
more and a number of other financial goals which were satisfied by the
consummation of our agreement with Elan and the completion of our stock offering
in April 2000. Additional increases are the result of increased expenses
necessary to manage and support our expanding product and business development
efforts. We expect general and administrative expenses to continue to increase
as a result of increasing legal and other professional fees in connection with
the overall scale-up of our operations, business development efforts and patent
protection.

     Interest income increased to $914,000 and $1.2 million for the three and
six months ended June 30, 2000, respectively, compared to $113,000 and $203,000
for the corresponding periods in 1999. The increase is due to higher average
balances in our cash and cash equivalents and securities available-for-sale
during the six and three month periods ending June 30, 2000, as compared to the
same periods in 1999. Cash balances were higher as a result of public offerings
completed in both July 1999 and April 2000 that resulted in $58.0 million net
proceeds and $5.0 million received in January 2000 for the sale of common stock
to Elan pursuant to our collaboration with Elan. Interest income generally
fluctuates as a result of the average amount of cash available for investment
and prevailing interest rates.

     Interest expense decreased and was income of $47,000 and expense of $91,000
for the three and six months ended June 30, 2000, compared to expense of
$149,000 and $261,000, respectively, for the corresponding periods in 1999. The
recorded income during the second quarter 2000 is due to our repayment of $6.9
million to Schering on a loan.

                                       9
<PAGE>

At Schering's option, the remaining balance of $997,000 was converted into
42,435 shares of our common stock in June 2000. However, interest expense is
expected to increase in the future as we arrange for additional financing for
operations.

     Equity in loss of unconsolidated affiliate was $1.8 million and $3.6
million for the three and six month periods ending June 30, 2000, respectively,
compared to $204,000 and $698,000 for the corresponding periods in 1999. The
expense in 2000 is our 80.1% share of Medizyme's first and second quarter
expenses. Our ownership in the Medizyme joint venture is 80.1% and as such we
are required to expense our share of their losses. Medizyme's expenses include
$1.25 million amortized expense in each quarter for payment of a $15.0 million
license fee paid to Elan in January 2000, as well as $972,000 and $960,000 we
invoiced in the first and second quarters, respectively, for research we
conducted on HERZYME(TM). The 1999 equity in loss of unconsolidated affiliate
was in connection with our initial cash investment of $2.0 million and the
subsequent transfer of our gene identification and target validation technology
to Atugen AG in 1998. At June 30, 1999, we owned 83.2% of Atugen's outstanding
common stock and, as a result, we recorded our share of Atugen's first and
second quarter net losses resulting in equity in loss of unconsolidated
affiliate of $494,000 and $204,000, respectively. In 1999, we completely
expensed our remaining investment in Atugen and therefore no expense related to
Atugen has been recorded during 2000.

Liquidity and Capital Resources

     We have financed our operations since inception through sales of equity
securities in public offerings, private placements of preferred and common
stock, funds received under our collaborative agreements and financing under
equipment and tenant improvement loans. From inception through June 30, 2000, we
have received approximately:

 .  $29.0 million in net proceeds from private placements;
 .  $89.1 million in net proceeds from public offerings;
 .  $82.1 million from our collaborations; and
 .  $9.8 million from equipment financing.

     We had cash, cash equivalents and securities available-for-sale of $63.6
million at June 30, 2000 compared with $14.0 million at December 31, 1999. The
$49.6 million increase in cash, cash equivalents and securities available-for-
sale is primarily the result of $2.3 million used for operations, net of
revenues of $7.8 million and $498,000 used for investments in equipment and
patents, offset by:

 .  $52.7 million received in the public offering of our common stock;
 .  $17 million received in a sale of preferred and common stock to a corporate
   collaborator;
 .  $12.0 million invested in Medizyme;
 .  $1.0 million in net borrowings;
 .  $6.9 million used to pay off a loan;
 .  $600,000 received for sales of common stock under option exercises; and
 .  $126,000 for payments on loan facilities.

     We invest our cash, cash equivalents and securities available-for-sale in
interest-bearing, investment grade securities.

     Accounts receivable at June 30, 2000 was $3.8 million compared to $2.0
million at December 31, 1999. Accounts receivable at June 30, 2000 included
$832,000 due from Chiron for reimbursement of

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<PAGE>

ANGIOZYME(TM) second quarter research, $1.9 million due from Medizyme for first
and second quarter HERZYME(TM) research, $863,000 due from Lilly for research
support for our anti-HCV ribozyme program and $164,000 due from Atugen for
administrative services and patent expenses. Accounts receivable at December 31,
1999 primarily consisted of $485,000 due from Atugen for administrative services
and patent expenses, $525,000 due from Eli Lilly for research support for our
anti-HCV ribozyme program and $1.0 million due from Chiron for reimbursement of
ANGIOZYME(TM) fourth quarter research. The outstanding receivables due from 1999
have been received in 2000.

     Total additions for property, plant and equipment for the three months
ending June 30, 2000 were $324,000, most of which were financed through our
existing equipment loan facility with Schering AG, described below. We
anticipate future capital needs to be financed by the Schering AG loan facility
for the next two years.

     In April 1997 we entered into a purchase agreement with Schering AG and
Schering Berlin Venture Corporation ("SBVC"), an affiliate of Schering AG,
subsequently amended, as part of our target discovery and validation program.
SBVC made a $2.5 million equity investment in us in April 1997 in exchange for
212,766 shares of common stock and made an additional equity investment of $2.5
million for 465,117 shares in April 1998. Separately, Schering AG provided loans
of $2.0 million in each of 1997, 1998 and 1999 and $1.0 million in February
2000. Schering AG has agreed to continue to provide loans of up to $2.0 million
annually through 2001, provided that the collaboration is continued. The loans,
which carry an interest rate of 8.0% per annum, are immediately convertible into
equity at the option of Schering AG. In April 2000, after the completion of a
public offering, we repaid $6.9 million of our outstanding borrowings from
Schering AG. In June 2000, Schering AG converted our remaining balance of
$997,000 into 42,435 shares of our common stock at a conversion price of $23.50.
If Schering AG does not continue the collaboration, we may need to seek
alternative sources of financing. Amounts not used in any calendar year may be
carried forward to future years. According to the terms of our agreement with
Schering AG, 50.0% of any borrowings on the line of credit must be
collateralized by equipment purchases. At June 30, 2000, we had no outstanding
loans from Schering AG. Principal and interest payments are deferred until
maturity of the loans in April 2004. As a result of the Atugen formation in
1998, we now subcontract all of our existing target discovery and identification
programs to Atugen; however, as long as our collaboration continues with
Schering AG we expect to continue to borrow against the loans.

     In July 1994, we entered into an agreement with Chiron to collaborate
exclusively on up to five specific targets selected by Chiron. Four targets are
currently subject to the exclusivity provision, including ANGIOZYME(TM).
Currently, ANGIOZYME(TM) is being developed in collaboration with Chiron and we
share equally all development costs and profits with Chiron. In 1999, we
recorded $4.0 million in revenues due from Chiron for reimbursement of expenses
incurred for the clinical development of ANGIOZYME(TM). During the first half of
2000, we recorded $2.2 million in revenues due from Chiron for ANGIOZYME(TM). We
expect total 2000 expenses related to ANGIOZYME(TM) to be approximately $11.0
million, of which Chiron is expected to reimburse us approximately $5.5 million.

     In March 1999, we entered into a collaboration with Eli Lilly to conduct
research, development and commercialization of our anti-HCV ribozyme for the
treatment of Hepatitis C virus infection. We granted Lilly the exclusive
worldwide right to develop and commercialize the anti-HCV ribozyme in return for
funding of all research, development and commercialization costs for the drug.
Under the terms of the agreement, we received approximately $9.2 million during
1999, which included $1.7 million of funding for research and clinical trial
expenses and a $7.5 million equity investment. In April 1999, Lilly purchased
five shares of our Series L convertible preferred stock for $7.5 million. Each
share of Series L convertible preferred stock is convertible into shares of our
common stock based upon milestones related to the development and
commercialization of the anti-HCV ribozyme. Depending on the achievement of
certain milestones, each share of convertible preferred stock will either
convert into $500,000 or $1.5 million of common stock valued at the average
closing price over the 30 days prior to conversion. During the six month period
ending June 30, 2000, we recorded $3.0 million in revenues

                                       11
<PAGE>

due from Lilly, which included $1.5 million in research revenues and $1.5
million for milestone payments relating to clinical development milestones for
the anti-HCV ribozyme. In 2000, we expect to receive approximately $2.9 million
for research in addition to the milestone payments of $1.5 million.

     In January 2000, we completed a joint venture with Elan for the development
and commercialization of HERZYME(TM), our potential product to treat breast and
other cancers. In accordance with the collaboration, we sold to Elan our Series
A convertible preferred stock for $12.0 million and, in turn, used those funds
for initial funding of Medizyme. Also as part of the collaboration, Elan
purchased 641,026 shares of our common stock for a purchase price of $5.0
million. Elan has also committed to purchase an additional $5.0 million of
common stock in April 2001 at a share price that is at a premium to the then
market price and would also be based on the achievement of certain milestones.
We have estimated that the development of HERZYME(TM) will require additional
funds of up to $15 million and, therefore, Elan has made available to us a
credit facility to fund our portion of Medizyme operating costs over a 30 month
period. Elan may convert this debt into shares of our Series B convertible
preferred stock in the future. During the period ending June 30, 2000, we
recorded revenues due from Medizyme of $1.9 million for research conducted for
the development of HERZYME(TM). In 2000, we expect to receive approximately $3.9
million in research revenues from Medizyme relating to our work on HERZYME(TM)
development.

     In April 2000, we completed a public offering of 3,150,000 shares of our
common stock that resulted in gross proceeds of $56.7 million. After underwriter
fees and expenses are deducted, net proceeds are expected to be approximately
$52.7 million. In April 2000 we repaid $6.9 million of our outstanding
borrowings from Schering AG with proceeds from this offering.

     We anticipate that the net proceeds from our offering, together with our
existing financial resources and expected revenues from our collaborations,
should be sufficient to meet our anticipated operating and capital requirements
through 2002. We expect to incur substantial additional costs, including:

 .  costs related to our research, drug discovery and development programs;
 .  preclinical studies and clinical trials of our products, if developed;
 .  prosecuting and enforcing patent claims;
 .  general administrative and legal items; and,
 .  manufacturing and marketing of products, if any.

     In the future we may raise additional capital through public or private
financing, as well as from new collaborative relationships, new credit
facilities and other sources.

                                       12
<PAGE>

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

     Not applicable.

PART II - OTHER INFORMATION

ITEM 2. CHANGES IN SECURITIES

     In April 2000, we completed a public offering of 3,150,000 shares of our
common stock for $18.00 per share that resulted in gross proceeds of $56.7
million. After underwriter fees and expenses are deducted, net proceeds are
expected to be approximately $52.7 million.

     On May 1, 2000 we amended our Certificate of Incorporation to authorize
60,000,000 shares of common stock, par value $0.01, pursuant to a vote of
shareholders on April 19, 2000. Our Board of Directors may issue authorized
shares of common stock from time to time as it determines desirable. Additional
issuances of common stock could dilute the ownership of current holders of
common stock.

     Pursuant to an agreement dated April 1997 between Ribozyme Pharmaceuticals
and Schering AG, Schering AG converted our outstanding borrowings of $997,206
into 42,435 shares of our common stock at a conversion price of $23.50 per share
on June 19, 2000.

     On July 3, 2000, we filed a Form S-3 Registration Statement to register
2,887,945 shares of our common stock for certain of our stockholders. We will
receive no proceeds from the sale of these shares by the selling stockholders.

                                       13
<PAGE>

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

     On April 19, 2000, we held our Annual Meeting of Shareholders. Matters
voted on and the results of such voting are as follows:

1.   The election of seven directors to hold office until the next Annual
     Meeting of Shareholders or until their respective successors shall be
     elected and qualified. The following persons were elected as our directors
     and received the number of votes set forth below:

     Director                           For                        Against
     --------                           ---                        -------
     Ralph E. Christoffersen            10,311,877                 347,360
     Jeremy Curnock Cook                10,313,543                 345,694
     John Groom                         10,313,543                 345,694
     David T. Morgenthaler              10,313,443                 345,794
     Samual Saks                        10,313,543                 345,694
     Anders P. Wiklund                  10,313,543                 345,694
     David Ichikawa                     10,313,543                 345,694

2.   Increase the number of authorized common shares from 20,000,000 to
     60,000,000.

          Votes for                         10,017,117
          Votes Against                        623,041
          Votes Abstained                       19,079

3.   To approve an increase in the number of options which may be granted under
     our Stock Option Plan by 750,000 from 2,017,154 to 2,767,154.

          Votes for                          5,066,527
          Votes Against                        918,240
          Votes Abstained                       35,142

4.   To ratify the selection of Ernst & Young, LLP as our independent auditors
     for the year ending December 31, 2000.

          Votes for                         10,614,456
          Votes Against                         23,630
          Votes Abstained                       21,151

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<PAGE>

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

     (a)  Exhibits

          3(i)   Amended and Restated Certificate of Incorporation (1)
          3(ii)  Restated Bylaws (2)
          10.1   Letter amending Employment Agreement dated July 6, 2000 between
                 Dr. Nassim Usman and the Company.
          10.2   Letter amending Employment Agreement dated July 6, 2000 between
                 Dr. Lawrence Blatt and the Company.

          (27)   Financial Data Schedule

     (b)  Reports on Form 8-K

     We filed a report on Form 8-K dated April 14, 2000, which reported the
closing of our stock offering of 3,150,000 shares of our common stock at $18.00
per share on April 11, 2000 for gross proceeds of $56.7 million.

     We filed a report on Form 8-K dated July 28, 2000, which reported the
following:

  .  On July 12, 2000, Ribozyme Pharmaceuticals, Inc. ("RPI"), announced results
     regarding opposition proceedings against one of its ribozyme patents in
     Europe (European Patent No. EP-B1 0291533).

  .  On July 18, 2000, RPI announced two promotions in its Research and
     Development organization.

  .  On July 20, 2000 RPI announced additional information regarding European
     Patent No. EP-B1 0291533.

  .  On July 21, 2000, RPI announced the receipt of a $1 million milestone
     payment from Eli Lilly and Company.

--------------------------------------------------------------------------------
(1) Incorporated by reference from the Company's Registration Statement on Form
    SB-2, file no. 333-34981, dated September 5, 1997.
(2) Incorporated by reference from the Company's Registration Statement on Form
    SB-2, file no. 333-1908-D, dated April 11, 1996.

                                       15
<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.

                                   RIBOZYME PHARMACEUTICALS, INC.

Dated: November 3, 2000               /s/ RALPH E. CHRISTOFFERSEN
       ----------------               ---------------------------
                                      Ralph E. Christoffersen
                                      President and Chief
                                      Executive Officer

Dated: November 3, 2000           By: /s/ LAWRENCE E. BULLOCK
       ----------------               -----------------------
                                      Lawrence E. Bullock
                                      Vice President and Chief Financial Officer
                                      (Principal Financial Officer and
                                      Principal Accounting Officer)

                                       16
<PAGE>

                                 Exhibit Index


    Exhibit                            Exhibit
      No.                            Description
      ---                            -----------
   3(I)      Amended and Restated Certificate of Incorporation (1)
   3(ii)     Restated Bylaws (2)
   10.1      Letter amending Employment Agreement dated July 6, 2000 between Dr.
             Nassim Usman and the Company.
   10.2      Letter amending Employment Agreement dated July 6, 2000 between Dr.
             Lawrence Blatt and the Company.
   27        Financial Data Schedule

____
(1)  Incorporated by reference from the Company's Registration Statement on Form
     SB-2, file no. 333-34981, dated September 5, 1997.
(2)  Incorporated by reference from the Company's Registration Statement on Form
     SB-2, file no. 333-1908-D, dated April 11, 1996.

                                      17