RIBOZYME PHARMACEUTICALS INC
S-3, 2000-07-03
PHARMACEUTICAL PREPARATIONS
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<PAGE>

     As filed with the Securities and Exchange Commission on July 3, 2000
                                                       Registration No. 333-
================================================================================
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

                                   FORM S-3
            REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933

                        RIBOZYME PHARMACEUTICALS, INC.
            (Exact Name of Registrant as Specified in its Charter)

<TABLE>
<S>                                   <C>                               <C>
            DELAWARE                              2834                        34-1697351
 (STATE OR OTHER JURISDICTION OF      (PRIMARY STANDARD INDUSTRIAL         (I.R.S. EMPLOYER
  INCORPORATION OR ORGANIZATION)       CLASSIFICATION CODE NUMBER)      IDENTIFICATION NUMBER)
</TABLE>

                             2950 WILDERNESS PLACE
                            BOULDER, COLORADO 80301
                                (303) 449-6500
  (Address, including zip code, and telephone number, including area code, of
                   registrant's principal executive offices)

                            RALPH E. CHRISTOFFERSEN
                     CHIEF EXECUTIVE OFFICER AND PRESIDENT
                             2950 WILDERNESS PLACE
                            BOULDER, COLORADO 80301
                                (303) 449-6500
(Name, address, including zip code, and telephone number, including area code,
                             of agent for service)

                                  Copies to:
                              Karen L. Witt, Esq.
                        Rothgerber Johnson & Lyons LLP
                      1200 Seventeenth Street, Suite 3000
                               Denver, CO 80202
                                (303) 623-9000

     Approximate date of commencement of proposed sale to the public: from time
to time after this Registration Statement becomes effective.

     If the only securities being registered on this form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box. [_]

     If any of the securities being registered on this form are to be offered on
a delayed or continuous basis pursuant to Rule 415 of the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. [X]

     If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. [_]

     If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [_]

     If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [_]

                        CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
        =====================================================================================================================
              Title of Shares        Amount to be        Proposed Maximum           Proposed Maximum          Amount of
             to be Registered         Registered     Offering Price Per Share   Aggregate Offering Price   Registration Fee
        ---------------------------------------------------------------------------------------------------------------------
        <S>                        <C>               <C>                        <C>                       <C>
         Common Stock, $0.01
         par value per share.....  2,887,188 Shares          $25.88                   $74,705,990             $19,722.38
        =====================================================================================================================
</TABLE>

(1)  Estimated solely for the purpose of calculating the registration fee in
     accordance with Rule 457(c) on the basis of the average of the high and low
     prices of the Common Stock as quoted on the Nasdaq National Market on June
     30, 2000.

        THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE
OR DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT
SHALL FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a),
MAY DETERMINE.
<PAGE>

     WE HAVE NOT AUTHORIZED ANYONE TO GIVE ANY INFORMATION OR MAKE ANY
REPRESENTATION ABOUT THE COMPANY THAT IS DIFFERENT FROM, OR IN ADDITION TO, THAT
CONTAINED IN THIS PROSPECTUS. THEREFORE, IF ANYONE DOES GIVE YOU INFORMATION OF
THIS SORT, YOU SHOULD NOT RELY ON IT. IF YOU ARE IN A JURISDICTION WHERE AN
OFFER TO SELL, OR THE SOLICITATION OF AN OFFER TO BUY, ANY OF THE SECURITIES
OFFERED BY THIS PROSPECTUS IS UNLAWFUL, OR IF YOU ARE A PERSON TO WHOM IT IS
UNLAWFUL TO DIRECT THESE KINDS OF ACTIVITIES, THE OFFER PRESENTED IN THIS
PROSPECTUS DOES NOT EXTEND TO YOU. THIS PROSPECTUS SPEAKS ONLY AS OF THE DATE OF
THIS PROSPECTUS UNLESS THE INFORMATION SPECIFICALLY INDICATES THAT ANOTHER DATE
APPLIES.


                               TABLE OF CONTENTS

                                                                      Page
                                                                      ----

RIBOZYME PHARMACEUTICALS, INC........................................    2
SELECTED FINANCIAL DATA..............................................    3
FORWARD-LOOKING STATEMENTS...........................................    3
RISK FACTORS.........................................................    4
USE OF PROCEEDS......................................................   12
SELLING STOCKHOLDERS.................................................   12
PLAN OF DISTRIBUTION.................................................   17
LEGAL MATTERS........................................................   19
EXPERTS..............................................................   20
WHERE YOU CAN FIND MORE INFORMATION..................................   20

                               _________________


                        RIBOZYME PHARMACEUTICALS, INC.






                               2,887,188 SHARES

                                 COMMON STOCK


                               _________________

                              P R O S P E C T U S
                               _________________







                                 July __, 2000

ANGIOZYME(TM) AND HERZYME(TM) are trademarks of Ribozyme Pharmaceuticals, Inc.
<PAGE>

     The information in this prospectus is not complete and may be changed. The
selling holders may not sell these securities until the registration statement
filed with the SEC is effective. This prospectus is not an offer to sell these
securities and is not soliciting an offer to buy these securities in any state
where the offer of sale is not permitted.

                   SUBJECT TO COMPLETION, DATED JULY 3, 2000

                                  PROSPECTUS
                                  ----------

                               2,887,188 Shares

                        RIBOZYME PHARMACEUTICALS, INC.
                                 Common Stock
                    Offered by Certain Selling Stockholders

     Certain of our stockholders have advised us that they intend to sell from
time to time up to 2,887,188 shares of our common stock, $0.01 par value per
share. No underwriter is underwriting this offering. The selling shareholders,
or their authorized transferees, may offer the shares from time to time in one
or more transactions on the Nasdaq National Market at prevailing market prices,
or in negotiated transactions at agreed upon prices, or in a combination of such
methods of sale. We provide more information about how the selling shareholders
may sell their shares in the section titled "Plan of Distribution" beginning on
page 17. We will receive no part of the proceeds of such sales. We originally
issued all of the shares offered by this document in private transactions from
February 1992 through March 2000. Those issuance of shares were exempt from the
registration requirements of the Securities Act of 1933, as amended, under
Section 4(2) of the Securities Act and Regulation D thereunder. We are
registering the shares as required by our various agreements with the selling
stockholders which are described in the section titled "Selling Stockholders"
beginning on page 12.

     Our common stock is traded on the Nasdaq National Market under the symbol
"RZYM." On June 30, 2000, the last reported sale price of our common stock on
the Nasdaq National Market was $25.81 per share. We do not know the prices at
which the selling shareholders will sell any of the shares, or the commissions
the selling shareholders will pay, if any, in connection with any such sale.
These prices and commissions may vary from transaction to transaction. We will
pay all expenses incident to offering and selling the shares to the public other
than any commissions and discounts of underwriters, dealers or agents and any
transfer taxes.

                              ___________________

     Investing in our common stock involves a high degree of risk.
     See "Risk Factors" beginning on page 4 for a discussion of
     certain factors that you should consider in connection with an
     investment in the securities.

     Neither the Securities and Exchange Commission nor any state
     securities commission has approved or disapproved these
     securities, or passed upon the adequacy or accuracy of this
     prospectus. Any representation to the contrary is a criminal
     offense.

                                July ___, 2000
<PAGE>

You should read the entire prospectus and the documents incorporated herein
carefully, including "Risk Factors" and the financial statements and related
notes, before making an investment decision. Unless otherwise noted, references
in this prospectus and the documents incorporated herein to "Ribozyme
Pharmaceuticals, "we," "our" and "us" refer to Ribozyme Pharmaceuticals, Inc., a
Delaware corporation, and its affiliates.


                        RIBOZYME PHARMACEUTICALS, INC.

     Following is a short summary of our business. You should carefully read our
Annual Report on Form 10-K for the year ended December 31, 1999, the Form S-3
Registration Statement (File No. 333-31456) filed by us on March 2, 2000, as
amended, and our Quarterly Report on Form 10-Q for the quarter ended March 31,
2000, which are incorporated herein by this reference, and the "Risk Factors"
section of this prospectus for more information on our business and the risks
involved in investing in our stock.

     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 messenger RNA, and thereby selectively inhibit protein
production or viral replication. Because many human diseases result from
abnormal protein production or viral replication, we believe that ribozymes may
prevent, treat or cure a broad range of human diseases.

     We are currently in clinical development and preclinical testing for the
following three product candidates:

     .    ANGIOZYME, for which we are conducting a Phase I/II clinical trial for
          the treatment of solid tumor cancers in collaboration with Chiron
          Corporation;

     .    an anti-HCV ribozyme which is being developed for the treatment of
          Hepatitis C in collaboration with Eli Lilly and Company; and

     .    HERZYME, which we are developing for the treatment of breast and other
          cancers in collaboration with Elan Corporation plc and its affiliates.

     We expect to identify and begin preclinical testing on an additional
product candidate by the end of 2000 and develop new ribozyme product candidates
in the future.

     Our strategy is to use our unique and patented ribozyme technology to
identify and develop a new class of drugs to treat human diseases for which
there are large numbers of patients and insufficient treatments. The principal
elements of our strategy are to:

     .    develop ribozyme drugs by pursuing multiple product candidates across
          a number of diseases;

                                      -2-
<PAGE>

     .    maximize value of new product candidates through expanded internal
          development;

     .    focus on human therapeutics and license other applications of our
          technology; and

     .    maintain and expand our patent portfolio and proprietary technology.

     Our corporate headquarters are located at 2950 Wilderness Place, Boulder,
Colorado 80301, and our telephone number is (303) 449-6500. Our web site address
is www.rpi.com. Information contained on our web site does not constitute part
of this prospectus.


                            SELECTED FINANCIAL DATA

     The yearly historical financial data for each of the five years in the
period ended December 31, 1999, have been taken, or are derived from, our
financial statements that have been audited by Ernst & Young LLP, independent
auditors, and are incorporated by reference herein and included in our Annual
Reports on Form 10-K for the years ended December 31, 1999, 1998 and 1997,
respectively. Historical financial data for the quarters ended March 31, 1999,
and March 31, 2000, is incorporated by reference from our Form 10-Q for the
period ended March 31, 2000. These historical results do not necessarily
indicate future results. It is important that you read our financial statements
and related notes, as well as the section "Management's Discussion and Analysis
of Financial Condition and Results of Operations" incorporated by reference from
our Form 10-K and Form 10-Q.


                          FORWARD-LOOKING STATEMENTS

     This prospectus and the documents incorporated herein by reference contain
statements which constitute "forward-looking statements" within the meaning of
Section 27A of the Securities Act of 1933, as amended (the "Securities Act"),
and Section 21E of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"). The words "anticipate," "expect," "believe," "goal," "plan,"
"intend," "estimate" and similar expressions and variations thereof used in this
prospectus are intended to specifically identify forward-looking statements.
Prospective investors are cautioned that any such forward-looking statements are
not guarantees of future performance and involve risks and uncertainties, and
that actual results may differ materially from those projected in the forward-
looking statements as a result of various factors, including the risk factors
described below. We undertake no obligation to publicly update or revise
forward-looking statements made in this prospectus or the documents incorporated
by reference herein to reflect events or circumstances after the date of this
prospectus or to reflect the occurrence of unanticipated events.

                                      -3-
<PAGE>

                                 RISK FACTORS

     You should carefully consider the following risk factors and all other
information contained in this prospectus, any prospectus supplement and the
documents incorporated by reference herein before purchasing our common stock.
Investing in our common stock involves a high degree of risk. Any of the
following risks could materially adversely affect our business, operating
results and financial condition and could result in a complete loss of your
investment.

We are a biotechnology company in the early stage of development and have only a
limited operating history for you to review in evaluating our business and
prospects.

     Our ribozyme technology is in an early stage of development and represents
a new and unproven approach to therapeutic products. There can be no assurance
that our technologies will enable us or any of our collaborators to discover and
develop therapeutic products.

     All of our products are in early stages of development, have never
generated any sales and require extensive testing before commercialization. We
do not expect any of our product candidates to be commercially available for at
least four years. You must consider, based on our limited history, our ability
to:

     .    obtain the financial resources necessary to develop, test, manufacture
          and market products;

     .    engage corporate partners to assist in developing, testing,
          manufacturing and marketing our products;

     .    satisfy the requirements of clinical trial protocols, including
          patient enrollment;

     .    establish and demonstrate the clinical efficacy of our products;

     .    obtain necessary regulatory approvals; and

     .    market our products to achieve acceptance and use by the medical
          community in general.

We have a history of losses, expect future losses and cannot assure you that we
will ever become or remain profitable.

     We have incurred significant losses and have had negative cash flows from
operations since inception. To date, we have dedicated most of our financial
resources to research and development and general and administrative expenses.
We have funded our activities primarily from sales of stock, revenues under
research and development agreements and lines of credit. As of March 31, 2000,
our accumulated deficit was $87.8 million.

                                      -4-
<PAGE>

     We expect to incur losses for at least the next several years because we
plan to spend substantial amounts on research and development of our products,
including preclinical studies and clinical trials, and, if we obtain necessary
regulatory approvals, on sales and marketing efforts.

We depend upon our collaborative relationships and our collaborators have rights
under these agreements which if exercised could adversely affect our ability to
develop our products and our operating results.

     Engaging corporate partners and other third parties to develop, test and
manufacture our initial products has been, and is expected to continue to be, a
key element of our strategy. Our current partners, Chiron Corporation, Eli Lilly
& Company and Elan Corporation plc, have the right to unilaterally terminate our
existing agreements or discontinue funding their share of product development
expenses. If any of them were to terminate its funding of the development of a
particular product, we may not have the right to continue development of that
product on our own.

     In addition, there are many aspects of our collaborations that have been
and will continue to be outside of our control including:

     .    decisions by our collaborators to extend or renew our agreements and
          relationships;

     .    the pace of development of our products including the achievement of
          performance milestones;

     .    development by our collaborators of competing technologies or
          products;

     .    exercise by our collaborators of marketing or manufacturing rights;
          and

     .    the loss of our rights to products or the profits from our products if
          we are unable to fund our share of development costs.

We have granted exclusive rights to certain of our collaborators to products
targeting specific gene sequences which could delay development of those
products and prevent us from entering into other collaborative agreements.

     Under our current collaborations, up to an aggregate of 50 targets may be
reserved at any time. Development of the products subject to these exclusivity
provisions is out of our control. These products will not be available to us
during the exclusivity term either to develop internally or in collaboration
with third parties.

     Some of our collaborators have the right to reserve exclusive rights to
specified products for a period of time, even if they are not developing that
product. Also, many of our

                                      -5-
<PAGE>

collaboration agreements require us to offer our collaborators a right of first
offer for certain targets and products.

Because we must obtain regulatory approval to market our products in the United
States and foreign jurisdictions, we cannot predict whether or when we will be
permitted to commercialize our products.

     The pharmaceutical industry is subject to stringent regulation by a wide
range of authorities. We cannot predict whether regulatory clearance will be
obtained for any product we develop. A pharmaceutical product cannot be marketed
in the United States until it has completed rigorous preclinical testing and
clinical trials and an extensive regulatory clearance process implemented by the
FDA. Satisfaction of regulatory requirements typically takes many years, is
dependent upon the type, complexity and novelty of the product and requires the
expenditure of substantial resources. Of particular significance are the
requirements covering research and development, testing, manufacturing, quality
control, labeling and promotion of drugs for human use.

     Before commencing clinical trials in humans, we must submit and receive
approval from the FDA of an Investigational New Drug application, or IND.
Clinical trials are subject to oversight by institutional review board and the
FDA and:

     .    must be conducted in conformance with the FDA's good laboratory
          practice regulations;

     .    must meet requirements for institutional review board oversight;

     .    must meet requirements for informed consent;

     .    must meet requirements for good clinical practices;

     .    are subject to continuing FDA oversight;

     .    may require large numbers of test subjects; and

     .    may be suspended by us or the FDA at any time if it is believed that
          the subjects participating in these trials are being exposed to
          unacceptable health risks or if the FDA finds deficiencies in the IND
          or the conduct of these trials.

     Before receiving FDA clearance to market a product, we must demonstrate
that the product is safe and effective on the patient population that will be
treated. Data obtained from preclinical and clinical activities are susceptible
to varying interpretations that could delay, limit or prevent regulatory
clearances. In addition, delays or rejections may be encountered based upon
additional government regulation from future legislation or administrative
action or changes in FDA policy during the period of product development,
clinical trials and FDA regulatory review.

                                      -6-
<PAGE>

Failure to comply with applicable FDA or other applicable regulatory
requirements may result in criminal prosecution, civil penalties, recall or
seizure of products, total or partial suspension of production or injunction, as
well as other regulatory action against our potential products or us.
Additionally, we have limited experience in conducting and managing the clinical
trials necessary to obtain regulatory approval.

     If regulatory clearance of a product is granted, this clearance will be
limited to those disease states and conditions for which the product is
demonstrated through clinical trials to be safe and efficacious. We cannot
ensure that any compound developed by us, alone or with others, will prove to be
safe and efficacious in clinical trials and will meet all the applicable
regulatory requirements needed to receive marketing clearance.

     Outside the United States, our ability to market a product is contingent
upon receiving a marketing authorization from the appropriate regulatory
authorities. This foreign regulatory approval process includes all of the risks
associated with FDA clearance described above.

     For additional information concerning regulatory approval of our
prospective products, see "Business--Government regulation of our drug
development activities" in our Form S-3 Registration Statement (File No. 333-
31456) filed with the SEC on March 2, 2000, as amended, which is incorporated
herein by reference.

We are involved in pending litigation and cannot at this time predict the
ultimate outcome or possible loss that could result from that litigation.

     We, along with our chief executive officer, are defendants in several
related lawsuits which purport to be class actions on behalf of purchasers of
our common stock on November 16 and 17, 1999. The lawsuits, which are
substantially identical, allege the defendants violated certain federal
securities laws based upon an allegedly misleading announcement made on November
15, 1999. Although we believe none of these legal proceedings have any merit, we
are unable to predict the ultimate outcome of these proceedings or determine the
total expense or possible loss, if any, that may ultimately be incurred in the
resolution of these proceedings.

If we cannot obtain additional financing, we may have to dilute your interest,
curtail our research and development, relinquish our rights to some or all of
our products or declare bankruptcy.

     Our existing financial resources and expected revenues from our
collaborations should be sufficient to meet our operating and capital
requirements through 2002; however, we may have to raise substantial additional
capital thereafter if:

     .    changes in our research and development plans cause unexpected large
          future expenditures; or

                                      -7-
<PAGE>

     .    changes in our collaborative relationships cause a significant
          reduction in our expected revenues from our collaborations.

     If we raise funds by selling more stock, your ownership share in us will be
diluted. We may grant future investors rights superior to those of the common
stock that you are purchasing. In addition, we do not know if additional funding
will be available or on acceptable terms when needed.

Our products require materials that may not be readily available or cost
effective, which may adversely affect our competitive position or profitability.

     The products we are developing are new chemical entities which are not yet
available in commercial quantities. Raw materials necessary for the manufacture
of our products may not be available in sufficient quantities or at a reasonable
cost in the future. Therefore, our products may not be available at a reasonable
cost in the future. In January 2000 we entered into an agreement with Avecia
Limited to manufacture ribozyme products for us based on technology we licensed
to them. Delays or failures in obtaining raw materials or in product
manufacturing, including deliveries from Avecia, could delay our product
submission for regulatory approval and our initiation of new development
programs which could, in turn, materially impair our competitive position and
potential profitability.

There is a significant degree of uncertainty relating to our patents that could
cause us to incur substantial costs and delays as a result of proceedings and
litigation regarding patents and other proprietary rights, possibly resulting in
additional expenses and the loss of some patent protection.

     Our basic patents, the Cech patents, expire in 2008 in the United States
and in 2007 in Europe and Japan. Although our license to these patents extends
through the expiration of the Cech patents or any extensions thereof, our
licensor preserves the right to terminate our license before such time under
certain circumstances. We have received approval of some additional patent
applications covering various aspects of the ribozyme technology, and we have
filed patent applications for other improvements and modifications which have
not yet been approved.

     We cannot be certain that the named inventors of subject matter claimed by
our patents and patent applications were the first to invent or the first to
file patent applications for these inventions. Furthermore, we cannot guarantee
that any patents will issue from any pending or future patent applications owned
by or licensed to us. Existing or future patents may be successfully challenged,
invalidated, found to be unenforceable, infringed upon, or circumvented by
others so that our patent rights would not create an effective competitive
barrier. We also cannot assure you that the scope of our issued patents will be
sufficiently broad to offer meaningful protection against competitive products.
We have filed documents in opposition of two patents granted to a competitor in
Europe. Competitors have filed documents in opposition of our Cech patents in
Europe and Japan. The patent opposition in Japan has been resolved in our

                                      -8-
<PAGE>

favor. The European opposition proceeding is in progress. We may not have
identified all United States and foreign patents that pose a risk of
infringement.

     We may be forced to litigate if an intellectual property dispute arises.
This litigation could be extremely expensive. Proceedings and litigation
involving our patents or patent applications also could result in adverse
findings about:

     .    the patentability of our inventions and product candidates; or

     .    the enforceability, validity or scope of protection provided by our
          patents.

     As discussed above, our competitors have taken the position in patent
oppositions and elsewhere that our patents are invalid or that our activities
infringe on their patent rights. While we do not believe we are infringing on
the patent rights of our known competitors, we may have to incur substantial
costs if litigation is brought against us by these competitors.

     The manufacture, use or sale of our products may infringe on the patent
rights of others. If we are unable to avoid infringing another party's patent
rights, we may be required to seek a license, defend an infringement action or
challenge the validity of the patents in court. Patent litigation is costly and
time consuming. We may not have sufficient resources to bring these actions to a
successful conclusion. In addition, if we do not obtain a license, do not
successfully defend an infringement action or are unable to have infringed
patents declared invalid, we may:

     .    incur substantial monetary damages;

     .    encounter significant delays in marketing our products; and

     .    be unable to participate in the manufacture, use or sale of products
          or methods of treatment requiring licenses.

     In addition, we regularly enter into agreements to in-license technologies
and patent rights. Should we fail to comply with the terms of those agreements,
including payment of any required maintenance fees or royalties, we would lose
the rights to those technologies and patents.

Disclosure of our trade secrets could hurt our competitive position.

     Because trade secrets and other unpatented proprietary information are
critical to our business, we attempt to protect our trade secrets by entering
into confidentiality agreements with third parties, employees and consultants.
However, these agreements can be breached and, if they are, there may not be an
adequate remedy available to us. In addition, third parties may independently
discover trade secrets and proprietary information. Costly and time-consuming
litigation could be necessary to enforce and determine the scope of our
proprietary rights.

                                      -9-
<PAGE>

We lack sales and marketing experience and will rely upon third parties to
market our products which will result in a loss of control over the marketing
process.

     We intend to rely on third parties with established direct sales forces to
market, distribute and sell many of our products. These third parties may have
significant control over important aspects of the commercialization of our
products, including market identification, marketing methods, pricing, sales
force recruitment and management and promotional activities. We may be unable to
control the actions of these third parties. We may be unable to make or maintain
arrangements with third parties to perform these activities on favorable terms.

Our success may depend on third-party reimbursement of patients' costs for our
products which could result in price pressure or reduced demand for our
products.

     Our ability to market products successfully will depend in part on the
extent to which various third parties are willing to reimburse patients for the
costs of our products and related treatments. These third parties include
government authorities, private health insurers and other organizations, such as
health maintenance organizations. Third-party payors are increasingly
challenging the prices charged for medical products and services. Accordingly,
if less costly drugs are available, third-party payors may not authorize or may
limit reimbursement for our products, even if our products are safer or more
effective than the alternatives. In addition, the trend toward managed
healthcare and government insurance programs could result in lower prices and
reduced demand for our products. Cost containment measures instituted by
healthcare providers and any general healthcare reform could affect our ability
to sell our products and may have a material adverse effect on us. We cannot
predict the effect of future legislation or regulation concerning the healthcare
industry and third-party coverage and reimbursement on our business.

You could experience substantial dilution in the future.

     You could experience dilution in the net tangible book value of the stock
held by you upon:

     .    the exercise by holders of outstanding options and warrants;

     .    the conversion by Schering AG of future outstanding debt into shares
          of our common stock;

     .    the conversion by Eli Lilly of our Series L convertible preferred
          stock into shares of our common stock; or

     .    the conversion by Elan of shares of our Series A convertible
          exchangeable preferred stock into a maximum of 1,200,000 shares of our
          common stock.

                                      -10-
<PAGE>

Our common stock has limited trading volume and a history of volatility which
could impair your investment.

     You may be unable to sell shares purchased in this offering at the time or
price desired. The market price of our common stock has fluctuated dramatically
in recent years. The trading price of our common stock may continue to fluctuate
substantially due to:

     .    quarterly variations in our operating results;

     .    our ability to raise additional funds;

     .    changes in the status of our corporate collaborative agreements;

     .    changes in earnings estimates by market research analysts;

     .    clinical trials of products;

     .    research activities, technological innovations or new products by us
          or our competitors;

     .    developments or disputes concerning patents or proprietary rights;

     .    purchases or sales of our stock by our executive officers, directors
          or substantial holders of our common stock;

     .    timing or denial by the FDA of clinical trial protocols or marketing
          applications;

     .    securities class actions or other litigation; and

     .    changes in government regulations.

     These fluctuations have sometimes been unrelated to our operating
performance. As a result, the value of your shares could vary significantly from
time to time. The historical trading volume of our common stock has been
limited. After this offering, an active public market for the common stock may
not develop or be sustained.

Both our corporate documents and Delaware law have anti-takeover provisions that
may discourage transactions involving actual or potential changes of control at
premium prices.

Our corporate documents:

     .    require procedures to be followed and time periods to be met for any
          stockholder to propose matters to be considered at annual meetings of
          stockholders, including nominating directors for election at those
          meetings; and

                                      -11-
<PAGE>

     .    authorize our Board of Directors to issue up to 5,000,000 shares of
          preferred stock without stockholder approval and to set the rights,
          preferences and other designations, including voting rights, of those
          shares as the Board of Directors may determine.

     In addition, we are subject to provisions of the Delaware General
Corporation Law that may make some business combinations more difficult.
Accordingly, transactions that otherwise could involve payment of a premium over
prevailing market prices to holders of common stock may be discouraged or more
difficult for our company than for other companies organized in other
jurisdictions.


                                USE OF PROCEEDS

     We will not receive any of the proceeds from the sale of the shares. All
proceeds from the sale of the shares will be for the account of the selling
stockholders, described below, or their authorized transferees. We will receive
proceeds of up to $9.0 million when Elan Corporation plc exercises its warrants
to purchase 500,000 shares of our common stock at an average exercise price of
$18.00 per share. See "Agreements with Selling Stockholders" beginning on page
14. We intend to use these proceeds for working capital and other general
corporate purposes.


                             SELLING STOCKHOLDERS

     We are registering the shares covered by this prospectus on behalf of the
selling stockholders named in the table below. We issued all of the shares to
the selling stockholders in private transactions from February 1992 through
March 2000, described at "Agreements with Selling Stockholders" below. We have
registered the shares to permit the selling stockholders and their pledgees,
donees, transferees or other successors-in-interest that receive their shares
from a selling stockholder as a gift, partnership distribution or other non-sale
related transfer after the date of this prospectus to resell the shares.

Shares Offered by Selling Stockholders

     The following table lists the selling stockholders for whose account the
shares are being offered, the number of shares (and percentage if greater than
one percent) of common stock held by the selling stockholder prior to the
offering, the number of shares being offered for the selling stockholder's
account, and (if greater than one percent) the percentage of the outstanding
common stock to be owned by such selling stockholder after completion of the
offering. The selling stockholders may sell some, all or none of their shares.
We do not know how long the selling stockholders will hold the shares before
selling them and we currently have no agreements, arrangements or understandings
with any of the selling stockholders regarding the sale of any of the shares.
The shares offered by this prospectus may be offered from time to time by the
selling stockholders.

                                      -12-
<PAGE>

<TABLE>
<CAPTION>
                                               Shares Beneficially                     Shares Beneficially
                                                    Owned Prior                             Owned After
                                                 to the Offering(1)       Shares        the Offering(1)(2)
                                             ------------------------                ------------------------
Name                                           Number        Percent     Offered       Number        Percent
----                                           ------        -------     -------       ------        -------
<S>                                          <C>             <C>        <C>          <C>             <C>
Elan International Services, Ltd.            2,142,276 (3)    12.8%     1,141,026    1,001,250         6.0%
International Biotechnology Trust            1,297,633 (4)     8.5%       537,633      760,000         5.0%
Chiron Corporation                           1,063,868 (5)     6.8%       619,424      444,444         2.8%
Innovir Laboratories, Inc.                     500,000 (6)     3.2%       150,000      350,000         2.2%
Schering Berlin Venture Corporation            397,972 (7)     2.6%       397,972            0           0%
Edgewater Lakewood, L.P.                        19,646 (8)       *         19,646            0           *
Morgenthaler Family Partnership                 15,101 (8)       *          5,101       10,000           *
European Molecular Biology Laboratory           10,000 (9)       *         10,000            0           *
LINC Capital, Inc.                               6,371(10)       *          6,371            0           *
Miroslav Anic                                       15(11)       *             15            0           *
                                             ---------                  ---------    ---------

     Total                                   5,452,882                  2,887,188    2,565,694
                                             =========                  =========    =========
</TABLE>

_______________________
*      Less than 1%.
(1)    Beneficial ownership is determined in accordance with rules of the SEC
       and includes shares over which the indicated beneficial owner exercises
       voting and/or investment power. Shares of common stock subject to options
       or warrants currently exercisable or exercisable within 60 days are
       deemed outstanding for computing the percentage ownership of the person
       holding the options but are not deemed outstanding for computing the
       percentage ownership of any other person. Except as otherwise indicated
       in the footnotes to this table, we believe that each stockholder
       identified in the table has sole voting and investment power with respect
       to all shares listed opposite their names. Unless otherwise indicated,
       the Selling Stockholders can be reached at the principal offices of
       Ribozyme Pharmaceuticals.
(2)    Assuming all of the shares registered for each selling stockholder are
       sold pursuant to this prospectus. See "Plan of Distribution."
(3)    Includes 1,001,250 shares convertible from our Series A preferred stock
       assuming a conversion price of $12.00 per share and 500,000 shares
       issuable upon exercise of warrants. Elan's offices are located at 102 St.
       James Court, Flatts, Smiths Parish, FL 04, Bermuda. John Groom is a
       director of Ribozyme Pharmaceuticals and a director, President and COO of
       Elan Corporation plc, the parent company of Elan.
(4)    International Biotechnology Trust plc's offices are located c/o
       Rothschild Asset Management, Ltd. at Five Arrows House, St. Swithin's
       Lane, London EC4N 8NR England. Jeremy Curnock Cook is a director of both
       Ribozyme Pharmaceuticals and International Biotechnology Trust.
(5)    Includes 444,444 shares issuable upon exercise of warrants. Chiron's
       offices are located at 4560 Horton Street, Emeryville, California 94608.
       David Ichikawa is a director of Ribozyme Pharmaceuticals and a Vice
       President of Chiron. Mr. Ichikawa disclaims beneficial ownership of these
       shares.
(6)    Includes 350,000 shares issuable upon exercise of warrants. Innovir's
       offices are located at 9 Parker, Irvine, California 92618.
(7)    Schering's offices are located at 340 Changebridge Road, Monteville, New
       Jersey 07045.
(8)    Mr. David T. Morgenthaler, a director of Ribozyme Pharmaceuticals, is a
       general partner of Morgenthaler Family Partnership and Edgewater
       Lakewood, L.P. and disclaims beneficial ownership of these shares except
       to the extent of his general partnership interests.
(9)    European Molecular Biology Laboratory's offices are located at
       Meyerhofstrasse 1, D-69117, Heidelberg, Germany.
(10)   LINC's offices are located at 303 East Wacker Drive, Suite 900, Chicago,
       Illinois 60601.
(11)   Mr. Anic's mailing address is 900 North Franklin, Suite 850, Chicago,
       Illinois 60610.

                                      -13-
<PAGE>

     The information in the table above with respect to the percentage of
outstanding common stock is based on the assumption that the number of
outstanding shares of common stock does not increase or decrease from
15,283,758, the number of shares of common stock used to prepare this table as
of June 20, 2000. It excludes:

     .    2,402,780 shares reserved for issuance under our stock option plan, of
          which 1,566,518 options to purchase shares were outstanding at a
          weighted average exercise price of $5.31 per share;

     .    1,311,269 shares issuable upon the exercise of outstanding warrants at
          a weighted average exercise price of $18.31 per share;

     .    297,030 shares issuable to Eli Lilly upon conversion of five shares of
          our Series L convertible preferred stock, based upon the closing price
          of $25.25 of our common stock on June 20, 2000;

     .    an undeterminable number of shares issuable to Elan in May 2001 for a
          total purchase price of $5.0 million;

     .    up to 1,200,000 shares issuable to Elan upon conversion of 12,015
          shares of our Series A convertible exchangeable preferred stock;

     .    an undeterminable number of shares issuable to Elan upon conversion of
          shares of our Series B convertible preferred stock that Elan may
          receive in the future upon conversion of our convertible promissory
          note to Elan;

     .    229,959 shares available for issuance under our 401(k) salary
          reduction plan and trust; and

     .    105,089 shares available for issuance under our employee stock
          purchase plan.

     We may amend or supplement this prospectus to update the disclosure set
forth herein.

Agreements with Selling Stockholders

Elan International Services, Ltd.
---------------------------------

     On January 7, 2000, we entered into a joint venture with Elan Corporation
plc, for the development and commercialization of HERZYME, our potential product
to treat breast and other cancers. As part of the joint venture, Medizyme
Pharmaceuticals Ltd., we contributed $12.0 million in initial funding to
Medizyme in exchange for 80.1 % of Medizyme's capital stock. Our capital
contribution was funded by our sale to Elan of our Series A convertible
exchangeable preferred stock for $12.0 million. The Series A preferred stock has
a dividend rate of 6.0%. At the end of the development period, expected to be
mid-2002, Elan has the right to exchange our

                                      -14-
<PAGE>

Series A preferred stock for 20.1% of the capital stock of Medizyme owned by us
or convert it prior to January 2006 into up to approximately 1.2 million shares
of our common stock.

     Elan purchased 641,026 shares of our common stock for $5.0 million and
committed to purchase an additional $5.0 million of common stock in May 2001 at
a per share price representing a premium of up to 30% of the price based on the
average closing price for the 45 trading days preceding the purchase, but not
less than such 45 trading-day average. In addition, Elan received warrants to
purchase 500,000 shares of our common stock at an average exercise price of
$18.00.

     Medizyme paid a license fee of $15.0 million to Elan for the use of its
MEDIPAD(R) drug delivery technology. As a result of this licensing transaction,
Medizyme has capitalized the entire license fee and is amortizing the balance
over the three-year term of the agreement. We will account for our investment in
Medizyme under the equity method. We have estimated that Medizyme will require
$15.0 million in funding through the development period to cover future
operating and development costs. Elan has provided us with a $12.0 million
credit facility on a draw-down basis to fund our portion of Medizyme's operating
costs over a 30-month period. Elan may convert this debt into shares of our
Series B convertible preferred stock. The Series B preferred stock has a
dividend rate of 12.0% and may be converted at any time 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.

     We entered into a Registration Rights Agreement with Elan International
Services, Ltd. in connection with the issuance of our securities to Elan.
Section 3 of this agreement grants "piggyback" registration rights to Elan at
any time that we propose to register our common stock under the Securities Act
of 1933, as amended. Elan has requested that we register 641,026 shares of
common stock and 500,000 shares of common stock underlying warrants held by
Elan.

Chiron Corporation
------------------

     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. Currently,
ANGIOZYME is being developed in collaboration with Chiron and in accordance with
the terms of agreement, we share equally all development costs and profits with
Chiron.

     In connection with our collaboration, we entered into a Subscription
Agreement pursuant to which we sold to Chiron shares of our common stock,
warrants to purchase shares of our common stock and shares of our Series E
preferred stock which were converted into shares of our common stock. Article IX
of this agreement grants registration rights to Chiron at any time that we
propose to register our stock under the Securities Act and when we become
eligible to register our shares on a Form S-3 Registration Statement.

                                      -15-
<PAGE>

Schering Berlin Venture Corporation
-----------------------------------

     In April 1997 we entered into a Purchase Agreement with Schering,
subsequently amended, as part of our target discovery and validation program.
Schering 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 provided
loans of $2.0 million in each of 1997, 1998 and 1999 and has agreed 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. In
April 2000, we repaid $6.9 million of our outstanding borrowings from Schering
with proceeds from our offering of 3,150,000 shares of common stock. On June 21,
2000, Schering converted our outstanding borrowings of $997,206 into 42,435
shares of our common stock at a conversion price of $23.50 per share.

     In April 2000, Schering sold 322,345 shares of our common stock as part of
the underwriters' over-allotment option in our public offering. In connection
with our public offering in April 2000, we agreed to file this Form S-3
Registration Statement to register the remaining shares of our common stock held
by Schering in exchange for Schering's agreement to waive its "piggyback"
registration rights under Section 11.02 of the Purchase Agreement dated April 9,
1997, as amended.

Innovir Laboratories, Inc. and European Molecular Biology Laboratory
--------------------------------------------------------------------

     In August 1999 we entered into an Asset Purchase Agreement with Innovir
and other entities pursuant to which we purchased certain technology and
intellectual property for the diagnosis and treatment of human disease in
exchange for $25,000 in cash, 160,000 shares of our common stock and warrants to
purchase up to 350,000 shares of our common stock. Innovir transferred 10,000
shares to European Molecular Biology Laboratory. Of the remaining 150,000 shares
held by Innovir, 16,000 shares are subject to an Escrow Agreement dated August
1999.

     Article 8 of the Asset Purchase Agreement grants registration rights to
Innovir and EMBL at any time that we propose to register our stock under the
Securities Act and when we become eligible to register our shares on a Form S-3
Registration Statement. However, Innovir and EMBL may not dispose of our common
stock until August 13, 2000, except for private resales or other dispositions to
persons or entities who agree in writing to be bound by these restrictions.
Innovir and EMBL have requested that we register the shares held by them.

LINC Capital, Inc. and Mr. Anic
-------------------------------

     In February 1993 we issued a Warrant to purchase 9,523 shares of common
stock to LINC Scientific Leasing ("LINC"). In October 1996 LINC assigned a
portion of this Warrant to Miroslav Anic. In March 2000 LINC exercised the
Warrant and paid the exercise price in Warrant Stock, as defined in the Warrant.
As a result, we issued 6,371 shares of our common stock to LINC and 15 shares of
our common stock to Mr. Anic. Article 12 of the Warrant grants

                                      -16-
<PAGE>

registration rights for the shares issued upon exercise of the Warrant at any
time we propose to register our securities under the Securities Act. LINC and
Mr. Anic have requested that we register the shares held by them.

Other Selling Stockholders
--------------------------

     In February 1992, December 1992 and June 1995 we entered into stock
purchase agreements with several investors for the purchase of our Series A,
Series B and Series G Preferred Stock, respectively, all of which were converted
into shares of our common stock in April 1996 upon the closing of our initial
public offering. Of these investors and successors-in-interest, the following
people and entities currently hold our common stock subject to registration
rights: International Biotechnology Trust, Morgenthaler Family Partnership and
Edgewater Lakewood, L.P. Article VIII of each agreement grants registration
rights to these stockholders.


                             PLAN OF DISTRIBUTION

     The shares covered by this prospectus may be offered and sold from time to
time by the selling stockholders. Each selling stockholder will act
independently of Ribozyme Pharmaceuticals in making decisions with respect to
the timing, manner and size of each sale. The selling stockholders may sell the
shares being offered on the Nasdaq National Market, or otherwise, at prices and
under terms then prevailing or at prices related to the then current market
price or at negotiated prices. The shares may be sold by one or more of the
following means of distribution:

     .    a block-trade in which a broker-dealer will attempt to sell shares as
          agent, but may position and resell a portion of the block as principal
          to facilitate the transaction;

     .    purchases by a broker-dealer as principal and resale by a broker-
          dealer for its own account pursuant to this prospectus;

     .    an over-the-counter distribution in accordance with the rules of the
          Nasdaq National Market;

     .    ordinary brokerage transactions and transactions in which the brokers
          solicit purchasers; and

     .    in privately negotiated transactions.

     To the extent required, this prospectus may be amended and supplemented
from time to time to describe a specific plan of distribution. If the plan of
distribution involves an arrangement with a broker-dealer for the sale of shares
through a block trade, special offering, exchange distribution or secondary
distribution or a purchase by a broker or dealer, the amendment or supplement
will disclose:

                                      -17-
<PAGE>

     .    the name of each selling stockholder and of the participating broker-
          dealer(s);

     .    the number of shares involved;

     .    the price at which the shares were sold;

     .    the commissions paid or discounts or concessions allowed to the
          broker-dealer(s), where applicable;

     .    that a broker-dealer(s) did not conduct any investigation to verify
          the information set out or incorporated by reference in this
          prospectus; and

     .    other facts material to the transaction.

     In connection with distribution of the shares or otherwise, the selling
stockholders may enter into hedging transactions with broker-dealers or other
financial institutions. In such transactions, broker-dealers or other financial
institutions may engage in short sales of our common stock in the course of
hedging the positions they assume with the selling stockholders. The selling
stockholders may also sell our common stock short and redeliver the shares to
close out such short positions. The selling stockholders may enter into options
or other transactions with broker-dealers or other financial institutions which
require the delivery to a broker-dealer or other financial institution of the
shares offered, which shares the broker-dealer or other financial institution
may resell pursuant to this prospectus (as supplemented or amended to reflect
such transaction). The selling stockholders may also pledge shares to a
broker-dealer or other financial institution, and, upon a default, such
broker-dealer or other financial institution may effect sales of the pledged
shares pursuant to this prospectus (as supplemented or amended to reflect such
transaction). In addition, any shares that qualify for sale pursuant to Rule 144
may be sold under Rule 144 rather than pursuant to this prospectus.

     From time to time, a selling stockholder may transfer, pledge, donate or
assign its shares of common stock to lenders or others and each of such persons
will be deemed to be a "selling stockholder" for purposes of this prospectus.
The number of shares of common stock beneficially owned by the selling
stockholder will decrease as and when it takes such actions. The plan of
distribution for the selling stockholders' shares of common stock sold under
this prospectus will otherwise remain unchanged, except that the transferees,
pledgees, donees or other successors will be selling stockholders hereunder.
Upon being notified by a selling stockholder that a donee or pledgee intends to
sell more than 500 shares, we will file a supplement to this prospectus.

     In effecting sales, brokers, dealers or agents engaged by the selling
stockholders may arrange for other brokers or dealers to participate. Brokers,
dealers or agents may receive commissions, discounts or concessions from the
selling stockholders in amounts to be negotiated prior to the sale. The brokers
or dealers and any other participating brokers or dealers may be deemed to be
"underwriters" within the meaning of Section 2(11) of the Securities Act of
1933, as amended, in connection with these sales, and any commissions, discounts
or concessions may

                                      -18-
<PAGE>

be deemed to be underwriting discounts or commissions under the Act. We will pay
all expenses incident to the offering of the shares to the public other than any
commissions and discounts of underwriters, dealers or agents and any transfer
taxes.

     The selling stockholders have advised us that they have not entered into
any agreements, understandings or arrangements with any underwriters or broker-
dealers regarding the sale of their securities. There is no underwriter or
coordinating broker acting in connection with the proposed sale of shares by the
selling stockholders.

     In order to comply with the securities laws of certain states, if
applicable, the shares must be sold in those jurisdictions only through
registered or licensed brokers or dealers. In addition, in certain states the
shares may not be sold unless they have been registered or qualified for sale in
the applicable state or an exemption from the registration or qualification
requirement is available and is complied with.

     Under applicable rules and regulations under the Securities Exchange Act of
1934, as amended, any person engaged in the distribution of the shares may not
simultaneously engage in market making activities with respect to our common
stock for a period of two business days prior to the commencement of the
distribution. In addition, each selling stockholder will be subject to
applicable provisions of the Exchange Act and the associated rules and
regulations under the Exchange Act, including Regulation M, which provisions may
limit the timing of purchases and sales of shares of our common stock by the
selling stockholders.

     We will make copies of this prospectus available to the selling
stockholders and have informed them of the need to deliver copies of this
prospectus to purchasers at or prior to the time of any sale of the shares.

     We will bear all costs, expenses and fees in connection with the
registration of the shares. The selling stockholders will bear all commissions
and discounts, if any, attributable to the sales of the shares. The selling
stockholders may agree to indemnify any broker-dealer or agent that participates
in transactions involving sales of the shares against specific liabilities,
including liabilities arising under the Securities Act. The selling stockholders
have agreed to indemnify specific persons, including broker-dealers and agents,
against specific liabilities in connection with the offering of the shares,
including liabilities arising under the Securities Act.

     We have agreed with the selling stockholders to keep the registration
statement of which this prospectus constitutes a part effective until the date
on which all of the shares may immediately be sold to the public without
registration pursuant to Rule 144(k) under the Act.


                                 LEGAL MATTERS

     The validity of the shares of common stock offered by this prospectus will
be passed upon for Ribozyme Pharmaceuticals by Rothgerber Johnson & Lyons LLP,
Denver, Colorado.

                                      -19-
<PAGE>

                                    EXPERTS

     The financial statements of Ribozyme Pharmaceuticals appearing in Ribozyme
Pharmaceuticals' Annual Report on Form 10-K for the year ended December 31,
1999, have been audited by Ernst & Young LLP, independent auditors, as set forth
in their report thereon included therein and incorporated herein by reference.
Such financial statements are incorporated herein by reference in reliance upon
such report given on the authority of such firm as experts in accounting and
auditing.


                      WHERE YOU CAN FIND MORE INFORMATION

     We have filed with the Securities and Exchange Commission a Registration
Statement under the Act, which registers the common stock being offered by this
prospectus. The Registration Statement, including its attached exhibits and
schedules, contains additional relevant information about us and our common
stock. The rules and regulations of the Commission allow us to omit certain
information included in the Registration Statement from this prospectus. Such
additional information is available for inspection and copying at the offices of
the Commission.

     We file annual, quarterly and current reports, proxy statements and other
information with the Commission. You may read and copy any reports, statements
or other information that we file at the following locations of the Commission:

Public Reference Room      New York Regional Office    Chicago Regional Office
Room 1024                  13th Floor                  Citicorp Center
450 Fifth Street, N.W.     7 World Trade Center        Suite 1400
Washington, D.C. 20549     New York, NY 10048          500 West Madison Street
                                                       Chicago, IL 60661

     Please call the Commission at l-800-SEC-0330 for further information. Our
public filings are also available from commercial document retrieval services
and at the Internet web site maintained by the Commission at http://www.sec.gov.

     The Commission allows us to "incorporate by reference" information into
this prospectus, which means that we can disclose important information to
investors by referring them to another document filed separately with the
Commission. The information incorporated by reference is deemed to be part of
this prospectus, except for any information superseded by information contained
directly in this document. This prospectus incorporates by reference the
documents set forth below that we have previously filed with the Commission.
These documents contain important information about us and our financial
condition.

     Form S-3 Registration Statement (File No. 333-31456).

                                      -20-
<PAGE>

     Ribozyme Pharmaceuticals Commission Filings (File No. 0-27914):

     .    Annual Report on Form 10-K for the year ended December 31, 1999.

     .    Quarterly Report on Form 10-Q for the quarter ended March 31, 2000.

     .    Current Report on Form 8-K dated April 14, 2000.

     The description of our common stock in our Registration Statement on Form
8-A dated April 11, 1996, including any amendments or reports filed for the
purpose of updating such description.

     All of the filings pursuant to the Exchange Act after the date of filing
the original Registration Statement and prior to the effectiveness of the
Registration Statement.

     You can obtain any of the documents incorporated by reference in, but not
included with, this prospectus from us without charge, excluding all exhibits
unless we have specifically incorporated by reference an exhibit in this
prospectus, by requesting them in writing or by telephone from the following
address:

     Ribozyme Pharmaceuticals
     Attention: Lawrence E. Bullock
     Vice President of Administration & Finance, CFO and Secretary
     2950 Wilderness Place
     Boulder, CO 80301
     Telephone (303) 449-6500

                                      -21-
<PAGE>

                PART II. INFORMATION NOT REQUIRED IN PROSPECTUS


ITEM 14.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The estimated expenses of the offering, all of which are to be borne by us,
are as following:

          Commission Filing Fee                        $   19,722
          Accounting Fees and Expenses                      6,000
          Legal Fees and Expense                           20,000
          Miscellaneous                                       278
                                                        _________
          TOTAL                                        $   46,000
                                                        =========

ITEM 15.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

     Article XI of our Bylaws provides for indemnification of our directors to
the fullest extent permitted by law, as now in effect or later amended. Article
XI of our Bylaws also permits the indemnification to the same extent of our
officers, employees or agents if, and to the extent, authorized by the Board of
Directors. In addition, the Bylaws provide for indemnification against expenses
incurred by a director to be paid by us at reasonable intervals in advance of
the final disposition of such action, suit or proceeding upon receipt of an
undertaking by or on behalf of the director or officer to repay such amount if
it shall be ultimately determined that he is not entitled to be indemnified by
us. The Bylaws further provide for a contractual cause of action on the part of
our directors for indemnification claims that have not been paid by us.

     Article VI of our Certificate of Incorporation, as amended, limits under
certain circumstances the liability of our directors for a breach of their
fiduciary duty as directors. These provisions do not eliminate the liability of
a director (1) for a breach of the director's duty of loyalty to us or our
stockholders, (2) for acts or omissions not in good faith or that involve
intentional misconduct or a knowing violation of law, (3) under Section 174 of
the General Corporate Law of the State of Delaware ("DGCL") (relating to the
declaration of dividends and purchase or redemption of shares in violation of
the DGCL) or (4) for any transaction from which the director derived an improper
personal benefit.

     Section 145 of the DGCL contains provisions regarding indemnification,
among others, of officers and directors. Section 145 of the DGCL provides in
relevant part:

     (a)  A corporation shall have power to indemnify any person who was or is a
          party or is threatened to be made a party to any threatened, pending
          or completed action, suit or proceeding, whether civil, criminal,
          administrative or investigative (other

                                      -22-
<PAGE>

          than an action by or in the right of the corporation) by reason of the
          fact that the person is or was a director, officer, employee or agent
          of the corporation, or is or was serving at the request of the
          corporation as a director, officer, employee or agent of another
          corporation, partnership, joint venture, trust or other enterprise,
          against expenses (including attorneys' fees), judgments, fines and
          amounts paid in settlement actually and reasonably incurred by the
          person in connection with such action, suit or proceeding if the
          person acted in good faith and in a manner the person reasonably
          believed to be in or not opposed to the best interests of the
          corporation, and, with respect to any criminal action or proceeding,
          had no reasonable cause to believe the person's conduct was unlawful.
          The termination of any action, suit or proceeding by judgment, order,
          settlement, conviction, or upon a plea of nolo contendere or its
          equivalent, shall not, of itself, create a presumption that the person
          did not act in good faith and in a manner which the person reasonably
          believed to be in or not opposed to the best interests of the
          corporation, and, with respect to any criminal action or proceeding,
          had reasonable cause to believe that the person's conduct was
          unlawful.

     (b)  A corporation shall have power to indemnify any person who was or is a
          party or is threatened to be made a party to any threatened, pending
          or completed action or suit by or in the right of the corporation to
          procure a judgment in its favor by reason of the fact that the person
          is or was a director, officer, employee or agent of the corporation,
          or is or was serving at the request of the corporation as a director,
          officer, employee or agent of another corporation, partnership, joint
          venture, trust or other enterprise against expenses (including
          attorneys' fees) actually and reasonably incurred by the person in
          connection with the defense or settlement of such action or suit if
          the person acted in good faith and in a manner the person reasonably
          believed to be in or not opposed to the best interests of the
          corporation and except that no indemnification shall be made in
          respect of any claim, issue or matter as to which such person shall
          have been adjudged to be liable to the corporation unless and only to
          the extent that the Court of Chancery or the court in which such
          action or suit was brought shall determine upon application that,
          despite the adjudication of liability but in view of all the
          circumstances of the case, such person is fairly and reasonably
          entitled to indemnity for such expenses which the Court of Chancery or
          such other court shall deem proper.

     (c)  To the extent that a present or former director or officer of a
          corporation has been successful on the merits or otherwise in defense
          of any action, suit or proceeding referred to in subsections (a) and
          (b) of this section, or in defense of any claim, issue or matter
          therein, such person shall be indemnified against expenses (including
          attorneys' fees) actually and reasonably incurred by such person in
          connection therewith.

     (d)  Any indemnification under subsections (a) and (b) of this section
          (unless ordered by a court) shall be made by the corporation only as
          authorized in the specific case

                                      -23-
<PAGE>

          upon a determination that indemnification of the present or former
          director, officer, employee or agent is proper in the circumstances
          because the person has met the applicable standard of conduct set
          forth in subsections (a) and (b) of this section. Such determination
          shall be made, with respect to a person who is a director or officer
          at the time of such determination, (1) by a majority vote of the
          directors who are not parties to such action, suit or proceeding, even
          though less than a quorum, or (2) by a committee of such directors
          designated by majority vote of such directors, even though less than a
          quorum, or (3) if there are no such directors, or if such directors so
          direct, by independent legal counsel in a written opinion, or (4) by
          the stockholders.

     Delaware law also permits a corporation to purchase and maintain insurance
on behalf of any person who is or was a director or officer against any
liability asserted against him and incurred by him in such capacity or arising
out of his status as such, whether or not the corporation has the power to
indemnify him against that liability under Section 145 of the DGCL.

     We also have provided liability insurance for each director and officer for
losses arising from claims or charges made against them while acting in their
capacities as our directors or officers.

     The above discussion of our corporate documents is not intended to be
exhaustive and is respectively qualified in its entirety by our corporate
documents.

ITEM 16.  Exhibits and Financial Statement Schedules

     (a)   Exhibits

     The following Exhibits are filed as a part of this Registration Statement
pursuant to Item 601 of Regulation S-K:

     Exhibit
     Number
     ------

     3.1       Amended and Restated Certificate of Incorporation of Ribozyme
               Pharmaceuticals dated April 17, 1996(1)

     3.2*      Articles of Amendment to the Certificate of Incorporation of
               Ribozyme Pharmaceuticals dated May 1, 2000

     3.2       Bylaws of Ribozyme Pharmaceuticals, as amended(2)

     4.1       Specimen Stock Certificate representing the common stock, par
               value $0.01 per share(2)

                                      -24-
<PAGE>

     4.2       Certificate of Designation, Preferences and Rights of Series L
               Preferred Shares (3)

     4.3       Certificate of Designations, Preferences & Rights of Series A
               Preferred Stock & Series B Preferred Stock (4)

     5.1*      Opinion of Rothgerber Johnson & Lyons LLP

     23.1*     Consent of Ernst & Young LLP, independent auditors

     23.2*     Consent of Rothgerber Johnson & Lyons LLP (included in Exhibit
               5.1 hereto)

     24.1*     Power of Attorney (included on signature page attached hereto)

____________________
*    Filed herewith
(1)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form SB-2 Registration Statement, File No. 333-34981.
(2)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form SB-2 Registration Statement, File No. 333-1908-D.
(3)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals', Form S-1 Registration Statement, File No. 333-75079.
(4)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form 8-K dated February 8, 2000.

     (b)   Financial Statement Schedules

     All schedules have been omitted because they are not applicable or not
required or the required information is included in the financial statements or
notes thereto.

ITEM 17.  UNDERTAKINGS.

     (a)   The undersigned registrant hereby undertakes:

           (1)  To file, during any period in which offers or sales are being
                made, a post-effective amendment to this registration statement
                to include any material information with respect to the plan of
                distribution not previously disclosed in the registration
                statement or any material change to such information in the
                registration statement;

           (2)  That, for the purposes of determining any liability under the
                Securities Act of 1933, each such post-effective amendment shall
                be deemed to be a new registration statement relating to the
                securities offered therein, and the offering of such securities
                at that time shall be deemed to be the initial bona fide
                offering thereof.

                                      -25-
<PAGE>

          (3)  To remove from registration by means of a post-effective
               amendment any of the securities being registered which remain
               unsold at the termination of the offering.

     (b)  The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or 15(d) of the Securities
Exchange Act of 1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of
1934) that is incorporated by reference in the registration statement shall be
deemed to be a new registration statement relating to the securities offered
therein, and the offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

     (c)  Insofar as indemnification for liabilities arising under the
Securities Act of 1933 may be permitted to directors, officers or persons
controlling the registrant pursuant to the foregoing provisions, or otherwise,
the registrant has been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable.

                                      -26-
<PAGE>

                                  SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Boulder, State of Colorado, on July 3, 2000.

                                     RIBOZYME PHARMACEUTICALS, INC.

                                     By:  /s/ RALPH E. CHRISTOFFERSEN
                                          --------------------------------------
                                          Ralph E. Christoffersen, Ph.D.
                                          Chief Executive Officer and President

     In accordance with the requirements of the Securities Act of 1933, as
amended, this Form S-3 Registration Statement has been signed below by the
following persons in the capacities and on the dates indicated. Each of the
following persons hereby appoints Ralph E. Christoffersen and Lawrence E.
Bullock, and each of them, as his attorney-in-fact to (1) execute and file
amendments for this Registration Statement, (2) request acceleration of the
effective date of our withdraw from the registration process this Registration
Statement or (3) take any other action regarding this Registration Statement as
such attorneys-in-fact, or either of them, may deem appropriate.

<TABLE>
<CAPTION>
Signature                          Title                                             Date
---------                          -----                                             ----
<S>                                <C>                                               <C>
/s/ RALPH E. CHRISTOFFERSEN        Chief Executive Officer and
---------------------------
Ralph E. Christoffersen, Ph.D.     President (Principal Executive Officer)           July 3, 2000

/s/ LAWRENCE E. BULLOCK            Vice President, Administration Finance,
-----------------------
Lawrence E. Bullock                Chief Financial Officer and Secretary
                                   (Principal Financial and Accounting Officer)      July 3, 2000

/s/ DAVID T. MORGENTHALER          Chairman of the Board of Directors                July 3, 2000
-------------------------
David T. Morgenthaler

/s/ JEREMY C. COOK                 Director                                          July 3, 2000
------------------
Jeremy C. Cook

/s/ DAVID ICHIKAWA                 Director                                          July 3, 2000
------------------
David Ichikawa

/s/ ANDERS WIKLUND                 Director                                          July 3, 2000
------------------
Anders Wiklund

/s/ JOHN GROOM                     Director                                          July 3, 2000
--------------
John Groom

/s/ SAMUEL R. SAKS                 Director                                          July 3, 2000
------------------
Samuel R. Saks, M.D.
</TABLE>

                                      -27-
<PAGE>

                                 EXHIBIT INDEX

Exhibit No.    Description

   3.1         Amended and Restated Certificate of Incorporation of Ribozyme
               Pharmaceuticals dated April 17, 1996(1)

   3.2*        Articles of Amendment to the Certificate of Incorporation of
               Ribozyme Pharmaceuticals dated May 1, 2000

   3.2         Bylaws of Ribozyme Pharmaceuticals, as amended(2)

   4.1         Specimen Stock Certificate representing the common stock, par
               value $0.01 per share(2)

   4.2         Certificate of Designation, Preferences and Rights of Series L
               Preferred Shares (3)

   4.3         Certificate of Designations, Preferences & Rights of Series A
               Preferred Stock & Series B Preferred Stock (4)

   5.1*        Opinion of Rothgerber Johnson & Lyons LLP

   23.1*       Consent of Ernst & Young LLP, independent auditors

   23.2*       Consent of Rothgerber Johnson & Lyons LLP (included in Exhibit
               5.1 hereto)

   24.1*       Power of Attorney (included on signature page attached hereto)

________________________
*    Filed herewith

(1)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form SB-2 Registration Statement, File No. 333-34981.

(2)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form SB-2 Registration Statement, File No. 333-1908-D.

(3)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals', Form S-1 Registration Statement, File No. 333-75079.

(4)  Documents incorporated by reference herein to certain exhibits to Ribozyme
     Pharmaceuticals' Form 8-K dated February 8, 2000.

                                     -28-


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