As filed with the Securities and Exchange Commission on February 9, 2001
Registration No. 333-
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SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

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

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MICROCIDE PHARMACEUTICALS, INC.
(EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

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DELAWARE 94-3186021
(STATE OR OTHER JURISDICTION OF (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION) IDENTIFICATION NUMBER)

850 MAUDE AVENUE
MOUNTAIN VIEW, CALIFORNIA 94043
(650) 428-1550
(ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
OF REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

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JAMES E. RURKA
PRESIDENT AND CHIEF EXECUTIVE OFFICER
MICROCIDE PHARMACEUTICALS, INC.
850 MAUDE AVENUE
MOUNTAIN VIEW, CALIFORNIA 94043
(650) 428-1550
(NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER,
INCLUDING AREA CODE, OF AGENT FOR SERVICE)

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Copies to:
ALAN MENDELSON, ESQ.
LATHAM & WATKINS
135 COMMONWEALTH DRIVE
MENLO PARK, CA 94025
(650) 328-4600

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APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC: As soon as
practical 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 under the Securities Act of
1933 other than securities offered only in connection with dividend or interest
reinvestment plans, please 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
=====================================================================
PROPOSED MAXIMUM
TITLE OF EACH CLASS OF AGGREGATE AMOUNT OF
SECURITIES TO BE REGISTERED OFFERING PRICE REGISTRATION FEE
- --------------------------- ---------------- -----------------

Common stock
$0.001 par value........... $35,000,000.00 $8,750.00
=====================================================================

(1) Estimated solely for the purpose of calculating the registration fee
pursuant to Rule 457(c) of the Securities Act.

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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 or until the Registration Statement shall become effective on
such date as the Commission, acting pursuant to said Section 8(a), shall
determine.

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================================================================================

PROSPECTUS

MICROCIDE PHARMACEUTICALS, INC.

$35,000,000 AGGREGATE AMOUNT OF COMMON STOCK

This prospectus will allow us to issue common stock over time. This means:

o we will provide a prospectus supplement each time we issue common
stock;

o the prospectus supplement will inform you about the specific terms of
that offering and also may add, update or change information contained
in this document; and

o you should read this document and any prospectus supplement carefully
before you invest.

Our common stock trades on the Nasdaq National Market under the symbol "MCDE."

Our address is 850 Maude Avenue, Mountain View, CA 94043, and our telephone
number is (650) 428-1550.

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THIS INVESTMENT INVOLVES A HIGH DEGREE OF RISK.
YOU SHOULD PURCHASE SHARES ONLY IF YOU CAN AFFORD A COMPLETE LOSS.

SEE "RISK FACTORS" BEGINNING ON PAGE 2.

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ON FEBRUARY 8, 2001, THE CLOSING SALE PRICE OF ONE SHARE OF MICROCIDE
COMMON STOCK AS QUOTED ON THE NASDAQ NATIONAL MARKET WAS $6.3125.

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NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE
SECURITIES COMMISSION HAS APPROVED OR DISAPPROVED OF
THESE SECURITIES OR DETERMINED IF THIS PROSPECTUS IS
TRUTHFUL OR COMPLETE. IT IS ILLEGAL FOR ANY
PERSON TO TELL YOU OTHERWISE.

THE DATE OF THIS PROSPECTUS IS FEBRUARY 9, 2001.

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PROSPECTUS SUMMARY

This summary highlights information incorporated by reference or contained
elsewhere in this prospectus. It is not complete and may not contain all of the
information that you should consider before investing in our securities. You
should read the entire prospectus carefully, including the "Risk Factors"
section, and you must consult the more detailed financial statements, and notes
to financial statements, incorporated by reference in this prospectus.

Whenever used herein, "our company," "we," "us," and "our" are references
collectively to Microcide Pharmaceuticals, Inc.

THE COMPANY

Microcide Pharmaceuticals, Inc. is a biopharmaceutical company whose
mission is to discover, develop and commercialize novel antimicrobials for the
improved treatment of serious bacterial, fungal and viral infections. Our
executive offices are located at 850 Maude Avenue, Mountain View, California
94043, and our telephone number is (650) 428-1550.

THE OFFERING

Common stock Offered in this prospectus................ __________ shares

Common stock Outstanding after the Offering(1)......... __________ shares

Use of Proceeds........................................ See "Use of Proceeds."

Proposed Nasdaq National Market symbol................. "MCDE"

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(1) Based on shares outstanding as of __________.

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4

RISK FACTORS

Before you purchase our securities, you should be aware that there are
risks, including those described below. You should consider carefully these risk
factors together with all of the other information contained elsewhere in this
prospectus or incorporated by reference before you decide to purchase our
securities.

WE MAY FAIL TO SUCCESSFULLY DEVELOP PHARMACEUTICAL PRODUCTS.

Our first potential pharmaceutical product, a cephalosporin compound,
commenced Phase I Clinical Trials under the direction of our partner, The R.W.
Johnson Pharmaceutical Research Institute, an affiliate of Johnson & Johnson, in
November 1999. The purpose of these studies is to assess the compound's safety,
tolerability and pharmacokinetics. Various modifications to the method of
administration of this compound are being explored. Based on data from three
Phase I protocols conducted to date, additional efforts to improve tolerability
will be undertaken which will extend completion of such Phase I trials to the
3rd Quarter of 2001, if not later. We may fail to successfully complete Phase I
trials for such cephalosporin compound. There are two other Microcide
cephalosporin compounds in the Johnson & Johnson collaboration: one in
pre-clinical development and the other, an orally-active cephalosporin, in the
research stage. Our other potential products are in the pre-clinical or research
stage. Our potential products will require significant additional research and
development efforts before we can sell them. These efforts include extensive
pre-clinical and clinical testing prior to submission to the FDA or other
regulatory authority. Pre-clinical and clinical testing will likely take several
years. After submission, such potential products will be subject to lengthy
regulatory review. We cannot predict with accuracy the time required to
commercialize new pharmaceutical products.

The development of new pharmaceutical products is highly uncertain and
subject to a number of significant risks. We do not expect any of our potential
products to be commercially available for a number of years, if at all.
Pharmaceuticals that appear to be promising at early stages of development may
not reach the market for a number of reasons including the following:

o we or our collaborators may not successfully complete our research and
development efforts;

o any pharmaceuticals we or our collaborators develop may be found to be
ineffective or to cause harmful side effects during pre-clinical
testing or clinical trials;

o we may fail to obtain required regulatory approvals for any products
we develop;

o we may be unable to manufacture enough of any potential products at an
acceptable cost and with appropriate quality;

o our products may not be competitive with other existing or future
products; and

o proprietary rights of third parties may prevent us from
commercializing our products.

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5

WE MAY BE UNABLE TO MAINTAIN OUR CURRENT CORPORATE COLLABORATIONS OR ENTER INTO
NEW COLLABORATIONS, WHICH COULD DELAY DEVELOPMENT OF OUR POTENTIAL PRODUCTS.

Our strategy for enhancing our research and development capability and
funding, in part, our capital requirements involves entering into collaboration
agreements with major pharmaceutical companies. We have entered into such
collaboration agreements with Johnson & Johnson, Daiichi Pharmaceutical Co.,
Ltd., Pfizer Inc. and Schering-Plough Animal Health Corporation. Under such
agreements, our collaborative partners are responsible for:

o selecting which compounds discovered in the collaboration will proceed
into subsequent development, if any;

o conducting pre-clinical testing, clinical trials and obtaining
required approvals for such potential products; and

o manufacturing and commercializing any such approved products.

We cannot control the timing of such actions or the amount of resources
devoted to such activities by our partners. In addition, these agreements are
subject to cancellation or the election not to extend by our partners. As a
result, our receipt of revenue (whether in the form of continued research
funding, product development milestones, or royalties on sales) depends upon the
decisions made and the actions taken by our partners. Our collaborative partners
may view compounds that we may discover as competitive with such partner's
products or potential products, and therefore such partner may elect not to
proceed with the development of our potential product. Our partners are free to
pursue their own existing or alternative technologies to develop products in
preference to our potential products. We cannot be certain that our interests
will continue to coincide with those of our partners, or that disagreements
concerning our rights, technology, or other proprietary interests will not arise
with our partners.

A large portion of our revenues to date have resulted from our
collaborations. We intend to continue to rely on our collaborations to fund a
substantial portion of our research and development activities over the next
several years. If our existing partners do not extend our collaborations or if
we are unable to enter into new collaborations, the development and
commercialization of our potential products may be delayed. In addition, we may
be forced to seek alternative sources of financing for such product development
and commercialization activities.

OUR DRUG DISCOVERY AND DEVELOPMENT PROGRAMS WILL REQUIRE SUBSTANTIAL ADDITIONAL
FUNDING.

The development of our potential pharmaceutical products will require
substantially more money than we currently have. We intend to seek to raise such
additional funding from sources including other collaborative partners and
through public or private financings involving the sale of equity or debt
securities. We cannot be certain that any financings will be available when
needed, or if available will be on acceptable terms. Funding from collaborative
partners could limit our ability to control the research, development and
commercialization of potential products, and could limit our revenues in profits
from such products, if any. Pursuant to such agreements we may be required to
give up rights to products or technologies that we would otherwise seek to
develop or commercialize ourselves. Any additional equity financing will result
in dilution

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to our current shareholders. If we fail to secure sufficient additional funding
we will have to delay or terminate some or all of our drug discovery and
development programs.

WE HAVE INCURRED SUBSTANTIAL LOSSES IN THE PAST AND EXPECT TO CONTINUE TO INCUR
LOSSES FOR THE NEXT SEVERAL YEARS.

We have incurred substantial net losses in every year since our inception
in December 1992. We had net losses of $4.6 million in 1997, $9.8 million in
1998, $10.7 million in 1999, and $10.5 million in the nine months ended
September 30, 2000. We had an accumulated deficit of $49.8 million through
September 30, 2000. We expect to continue to incur operating losses over the
next several years.

Substantially all of our revenues to date have resulted from license fees,
research support and milestone payments under our collaborative agreements. We
will not receive revenues or royalties from drug sales until we or our
collaborative partners successfully complete clinical trials with regard to a
drug candidate, obtain regulatory approval for such drug candidate, and
successfully commercialize the drug. We do not expect to receive revenues or
royalties from sales of drugs for a number of years, if at all. If we fail to
achieve sufficient revenues to become profitable or sustain profitability, we
may be unable to continue operations.

OUR APPROACH TO DRUG DISCOVERY IS UNPROVEN AND WE MAY NOT SUCCEED IN IDENTIFYING
ANY DRUG CANDIDATES WITH CLINICAL BENEFITS.

We are developing a gene function based technology platform and other
proprietary technology to attempt to identify and commercialize novel
antibiotics, antifungals and antiviral agents. To date these technologies have
identified a small number of compounds that have demonstrated potential clinical
benefits. We cannot be certain that these or any other technology we may develop
will allow us to identify drug candidates that may have clinical benefits. The
failure to identify and develop new drug candidates will have a material adverse
effect on our business.

WE MAY FAIL TO SATISFY SAFETY AND EFFICACY REQUIREMENTS IN OUR CLINICAL TRIALS
FOR OUR POTENTIAL PRODUCTS.

Either we or our collaborators must show through pre-clinical studies and
clinical trials that each of our pharmaceutical products is safe and effective
in humans for each indication before obtaining regulatory clearance from the FDA
for the commercial sale of that pharmaceutical. If we fail to adequately show
the safety and effectiveness of a pharmaceutical, regulatory approval could be
delayed or denied. The results from pre-clinical studies and early clinical
trials are often different than the results that are obtained in large-scale
testing. We cannot be certain that we will show sufficient safety and
effectiveness in our clinical trials that would allow us to obtain the needed
regulatory approval. A number of companies in the pharmaceutical industry,
including biotechnology companies, have suffered significant setbacks in
advanced clinical trials, even after promising results in earlier trials.

Any drug is likely to produce some level of toxicity or undesirable side
effects in animals and in humans when administered at sufficiently high doses
and/or for a long period of time. Unacceptable toxicities or side effects may
occur in the course of toxicity studies or clinical trials. We have observed
local irritation at the injection site in some subjects receiving our
cephalosporin product in Phase I clinical trials. This will require additional
efforts to improve tolerability, thereby extending the time to complete such

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Phase I trials. If we observe unacceptable toxicities or other side effects, we,
our collaborators or regulatory authorities may interrupt, limit, delay or halt
the development of the drug. In addition, such unacceptable toxicities or side
effects could prevent approval by the FDA or foreign regulatory authorities for
any or all indications.

We must obtain regulatory approval before marketing or selling our future
drug products. In the United States, we must obtain FDA approval for each drug
that we intend to commercialize. The FDA approval process is lengthy and
expensive, and approval is never certain. Products distributed abroad are also
subject to foreign government regulation. The process of obtaining FDA and other
required regulatory approvals can vary a great deal based upon the type,
complexity and novelty of the products involved. 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 clinical
trials and FDA regulatory review. Similar delays also may be encountered in
foreign countries.

None of our drug candidates has received regulatory approval. If we fail to
obtain this approval, we will be unable to commercially manufacture and sell our
drug products. Even if we obtain regulatory approval, we may be required to
continue clinical studies even after we have started selling a pharmaceutical.
In addition, identification of certain side effects after a drug is on the
market or the occurrence of manufacturing problems could cause subsequent
withdrawal of approval, reformulation of the drug, additional pre-clinical
testing or clinical trials and changes in labeling of the product. This could
delay or prevent us from generating revenues from the sale of that drug or cause
our revenues to decline.

If we obtain regulatory approval, we will also be subject to ongoing
existing and future FDA regulations and guidelines and continued regulatory
review. In particular, we, our collaborators, or any third party that we use to
manufacture the drug will be required to adhere to regulations setting forth
current good manufacturing practices. The regulations require that we
manufacture our products and maintain our records in a particular way with
respect to manufacturing, testing and quality control activities. Furthermore,
we, our collaborators, or our third-party manufacturers must pass a pre-approval
inspection of manufacturing facilities by the FDA before obtaining marketing
approval.

Failure to comply with the FDA or other relevant regulatory requirements
may subject us to administrative or legally imposed restrictions. These include:
warning letters, civil penalties, injunctions, product seizure or detention,
product recalls, total or partial suspension of production and FDA refusal to
approve pending New Drug Applications, or NDAs, or supplements to approved NDAs.

WE DEPEND ON EFFECTIVELY PROTECTING OUR INTELLECTUAL PROPERTY.

Our success depends in part on our ability to establish, protect and
enforce our proprietary rights relating to our lead compounds, gene discoveries,
screening technology and certain other proprietary technology. We have filed
approximately 80 patent applications in the United States, in addition to
applications filed in other countries, in order to protect lead compounds, gene
discoveries and screening technology, and 22 United States patents have been
issued to date on such applications. The patent position of biotechnology and
pharmaceutical companies is highly uncertain and involves many complex legal and
technical issues. We cannot be certain that patents will be granted with respect
to any of our patent applications currently pending in the United States or in
other countries, or with respect to applications filed in the future. Our
failure to obtain patents pursuant to our current or future applications could
have a material adverse effect on our business. Furthermore, we cannot be
certain that any patents issued to us will not be

-5-

infringed, challenged, invalidated or circumvented by others, or that the rights
granted thereunder will provide competitive advantages to us. In particular, it
is difficult to enforce patents covering methods of use of screening and other
similar technologies. Litigation to establish the validity of patents, to defend
against copatent infringement claims and to assert infringement claims against
others can be expensive and time-consuming, even if the outcome is favorable to
us. If the outcome of patent prosecution or litigation is not favorable to us,
our business could be materially adversely affected.

Our commercial success also depends on our ability to operate without
infringing patents and proprietary rights of third parties. There can be no
assurance that our products will not infringe on the patents or proprietary
rights of others. We may be required to obtain licenses to patents or other
proprietary rights of others. Such licenses may not be available on terms
acceptable to us, if at all. The failure to obtain such licenses could delay or
prevent our collaborative partners' activities, including the development,
manufacture or sale of drugs requiring such licenses.

In addition to patent protection, we rely on trade secrets, proprietary
know-how and technological advances which we seek to protect, in part, by
confidentiality agreements with our collaborative partners, employees, and
consultants. There can be no assurance that these agreements will not be
breached, that we would have adequate remedies for any such breach, or that our
trade secrets, proprietary know-how and technological advances will not
otherwise become known or be independently discovered by others.

OUR INDUSTRY IS HIGHLY COMPETITIVE.

We operate in a field in which new developments are occurring at an
increasing pace. Competition from biotechnology and pharmaceutical companies,
joint ventures, academic and other research institutions and others is intense
and is expected to increase. Many of our competitors have substantially greater
financial, technical and personnel resources than we have. Although we believe
that we have identified new and distinct approaches to drug discovery, there are
other companies with drug discovery programs, at least some of the objectives of
which are the same as or similar to ours. Competing technologies may be
developed which would render our technologies obsolete or non-competitive. We
are aware of many pharmaceutical and biotechnology companies that are engaged in
efforts to treat each of the infectious diseases for which we are seeking to
develop therapeutic products. There can be no assurance that our competitors
will not develop competing drugs that are more effective than those developed by
us and our collaborative partners or obtain regulatory approvals of their drugs
more rapidly than we and our collaborative partners, thereby rendering our and
our collaborative partners' drugs obsolete or noncompetitive. Moreover, there
can be no assurance that our competitors will not obtain patent protection or
other intellectual property rights that would limit our and our collaborative
partners' ability to use our technology or commercialize our or their drugs.

OUR POTENTIAL PRODUCTS MAY NOT BE ACCEPTABLE IN THE MARKET OR ELIGIBLE FOR THIRD
PARTY REIMBURSEMENT.

Any products successfully developed by us or our collaborative partners may
not achieve market acceptance. The antibiotic products which we are attempting
to develop will compete with a number of well-established traditional antibiotic
drugs manufactured and marketed by major pharmaceutical companies. The degree of
market acceptance of any of our products will depend on a number of factors,
including:

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o the establishment and demonstration in the medical community of the
clinical efficacy and safety of such products,

o the potential advantage of such products over existing treatment
methods, and

o reimbursement policies of government and third-party payors.

Physicians, patients or the medical community in general may not accept or
utilize any products that may be developed by us or our collaborative partners.
Our ability to receive revenues and income with respect to drugs, if any,
developed through the use of our technology will depend, in part, upon the
extent to which reimbursement for the cost of such drugs will be available from
third-party payors, such as government health administration authorities,
private health care insurers, health maintenance organizations, pharmacy
benefits management companies and other organizations. Third-party payors are
increasingly challenging the prices charged for pharmaceutical products. If
third-party reimbursement was not available or sufficient to allow profitable
price levels to be maintained for drugs developed by us or our collaborative
partners, it could adversely affect our business.

WE DO NOT HAVE MANUFACTURING, MARKETING OR SALES CAPABILITIES.

We do not have any experience in the manufacture of commercial quantities
of drugs, and our current facilities and staff are inadequate for the commercial
production or distribution of drugs. We intend to rely on our collaborative
partners for the manufacturing, marketing and sales of any products which result
from such collaborations. The current third-party manufacturer of our
beta-lactam potential product has in the past encountered difficulties with the
manufacture of such compound in sufficient quantities for clinical trial
purposes. Manufacturers often encounter difficulties in scaling up to
manufacture commercial quantities of pharmaceutical products. We cannot be
certain that our current or any other manufacturer will not encounter similar
delays in the scale-up to manufacture this or any other compound in commercial
quantities in the future.

We will be required to contract with third parties for the manufacture of
our products or to acquire or build production facilities before we can
manufacture any such products. There can be no assurance that we will be able to
enter into such contractual manufacturing arrangements with third parties on
acceptable terms, if at all, or acquire or build such production facilities
ourselves.

To date we have no experience with sales, marketing or distribution. In
order to market any of our products, we will be required to develop marketing
and sales capabilities, either on our own or in conjunction with others. We
cannot be certain that we will be able to develop any of these capabilities.

HEALTH CARE REFORM MEASURES MAY IMPACT PHARMACEUTICAL PRICING.

The levels of revenue and profitability of pharmaceutical companies may be
affected by continuing governmental efforts to contain or reduce the costs of
health care through various means. For example, in certain foreign markets
pricing or profitability of prescription pharmaceuticals is already subject to
governmental control. In the United States, there have been, and we expect that
there will continue to be, a number of federal and state proposals to implement
similar governmental control. Cost control initiatives could decrease the price
that we or our collaborative partners receive for any products which we or they
may develop in the future which would adversely affect our business. Further, to
the extent that such proposals or

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initiatives have a material adverse effect on our collaborative partners or
potential collaborative partners, our ability to commercialize our potential
products may be materially adversely affected.

WE MAY EXPERIENCE PRODUCT LIABILITY CLAIMS.

We face an inherent business risk of exposure to potential product
liability claims in the event that drugs, if any, developed through the use of
our technology are alleged to have caused adverse effects on patients. Such risk
exists for products being tested in human clinical trials, as well as products
that receive regulatory approval for commercial sale. We will, if appropriate,
seek to obtain product liability insurance with respect to drugs developed by us
and our collaborative partners. However, we may not be able to obtain such
insurance. Even if such insurance is obtainable, it may not be available at a
reasonable cost or in a sufficient amount to protect us against liability.

WE DEPEND ON KEY PERSONNEL.

We are highly dependent on management and scientific staff, including James
E. Rurka, our President and Chief Executive Officer, George H. Miller, Ph.D.,
our Senior Vice President - Research and Development, Donald D. Huffman, our
Vice President of Finance and Corporate Development and on our other executive
officers. Loss of the services of any key individual could have an adverse
effect on the Company. We do not carry key-man life insurance on any of our
executives. We believe that our future success will depend, in part, on our
ability to attract and retain highly talented managerial and scientific
personnel and consultants. We face intense competition for such personnel from,
among others, biotechnology and pharmaceutical companies, as well as academic
and other research institutions. We cannot be certain that we will be able to
attract and retain the personnel we require on acceptable terms.

WE ARE SUBJECT TO STRINGENT REGULATIONS RELATING TO HAZARDOUS MATERIALS.

As with many biotechnology and pharmaceutical companies, our activities
involve the use of radioactive compounds and hazardous materials. As a
consequence, we are subject to numerous environmental and safety laws and
regulations. Any violation of, and the cost of compliance with, these
regulations could materially adversely affect our operations. We are subject to
periodic inspections for possible violations of any environmental or safety law
or regulation.

WE HAVE CERTAIN ANTI-TAKEOVER PROVISIONS IN OUR CHARTER AND BYLAWS.

Certain provisions of our Restated Certificate of Incorporation and Bylaws
may have the effect of making it more difficult for a third party to acquire, or
discouraging a third party from attempting to acquire, control of our company.
Such provisions could limit the price that certain investors might be willing to
pay in the future for shares of our Common stock. Certain of these provisions
allow us to issue Preferred Stock without any vote or further action by the
stockholders, provide for staggered elections of our Board of Directors and
specify procedures for director nominations by stockholders and submission of
other proposals for consideration at stockholder meetings. None of these
provisions provide for cumulative voting in the election of directors. Certain
provisions of Delaware law applicable to us could also delay or make more
difficult a merger, tender offer or proxy contest involving us, including
Section 203 of the Delaware General Corporation Law, which prohibits a Delaware
corporation from engaging in any business combination with any stockholder
owning fifteen percent or more of the Company's outstanding voting stock
("interested

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stockholder") for a period of three years from the date a stockholder becomes an
interested stockholder unless certain conditions are met. The possible issuance
of Preferred Stock, the procedures required for director nominations and
stockholder proposals and Delaware law could have the effect of delaying,
deferring or preventing a change in control of Microcide, including without
limitation, discouraging a proxy contest or making more difficult the
acquisition of a substantial block of our Common stock. These provisions could
also limit the price that investors might be willing to pay in the future for
shares of our Common stock.

VOLATILITY OF STOCK PRICE.

The market price of the common stock, like that of the securities of many
other biopharmaceutical companies, has been and is likely to continue to be
highly volatile. The stock market has experienced significant price and volume
fluctuations that are often unrelated to the operating performance of particular
companies. Factors contributing to such volatility include:

o results of pre-clinical studies and clinical trials by us or our
competitors;

o announcements of new collaborations;

o announcements of our technological innovations or new therapeutic
products or that of our competitors;

o developments in our patent or other proprietary rights or that of our
competitors, including litigation;

o governmental regulation; and

o healthcare legislation.

Fluctuations in our operating results and market conditions for
biotechnology stocks in general could have a significant impact on the
volatility of the market price for the common stock and on the future price of
the common stock.

WE HAVE NO INTENTION TO PAY DIVIDENDS.

We have never paid any cash dividends on Microcide common stock. We
currently intend to retain all future earnings, if any, for use in our business
and do not expect to pay any dividends in the foreseeable future.

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FORWARD-LOOKING STATEMENTS

This prospectus and the documents incorporated by reference contain
forward-looking statements. In some cases, these statements can be identified by
the use of forward-looking terminology such as "may," "will," "could," "should,"
"would," "expect," "anticipate," "continue" or other similar words. These
statements discuss future expectations, contain projections of results of
operations or of financial condition or state trends and known uncertainties or
other forward-looking information. Such statements are based on current
expectations that involve a number of uncertainties including those set forth in
the risk factors above. When considering forward-looking statements, you should
keep in mind that the risk factors noted above and other factors noted
throughout this prospectus or incorporated by reference could cause our actual
results to differ significantly from those contained in any forward-looking
statement. We undertake no obligation to publicly revise these forward-looking
statements to reflect events or circumstances that arise after the date hereof.

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USE OF PROCEEDS

We cannot guarantee that we will receive any proceeds in connection with
this offering.

We intend to use the net proceeds of this offering, if any, for our
research, drug discovery and development programs and for other general
corporate purposes. Expenses to be funded with the offering proceeds, if any,
include research and development, the cost of pre-clinical and clinical studies,
and the production of compounds for such studies. The amounts actually expended
for each purpose may vary significantly depending upon numerous factors,
including the amount and timing of the proceeds from this offering, progress of
our research, drug discovery and development programs, the results of
pre-clinical and clinical studies, the timing of regulatory approvals,
technological advances, determinations as to commercial potential of our
compounds and the status of competitive products. In addition, expenditures will
also depend upon the establishment of collaborative research arrangements with
other companies and other factors.

As of the date of this prospectus, we cannot specify with certainty the
particular uses for the net proceeds, if any, to be received upon consummation
of this offering. Accordingly, our management will have broad discretion in the
application of any net proceeds received. Pending such uses, we intend to invest
the net proceeds, if any, from this offering in short-term, interest-bearing,
investment grade securities.

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14
PLAN OF DISTRIBUTION

We may offer the common stock:

- directly to purchasers;

- to or through underwriters;

- through dealers, agents or institutional investors; or

- through a combination of such methods.

Regardless of the method used to sell the common stock, we will provide a
prospectus supplement that will disclose:

- the identity of any underwriters, dealers, agents or institutional
investors who purchase the common stock;

- the material terms of the distribution, including the number of shares
sold and the consideration paid;

- the amount of any compensation, discounts or commissions to be
received by the underwriters, dealers, agents or institutional
investors;

- the terms of any indemnification provisions, including indemnification
from liabilities under the federal securities laws; and

- the nature of any transaction by an underwriter, dealer or agent
during the offering that is intended to stabilize or maintain the market
price of the common stock.

We will bear the expenses incident to the registration of the shares,
other than selling discounts and commissions. These expenses are estimated to
be $150,000.

-12-
15

LEGAL MATTERS

The validity of the issuance of the common stock offered in this prospectus
will be passed upon for us by Latham & Watkins, Menlo Park, California. Latham &
Watkins does not beneficially own any shares of our common stock as of the date
of this prospectus.

EXPERTS

Ernst & Young LLP, independent auditors, have audited our financial
statements included in our Annual Report on Form 10-K for the year ended
December 31, 1999, as set forth in their report, which is incorporated by
reference in this prospectus and elsewhere in the registration statement. Our
financial statements are incorporated by reference in reliance on Ernst & Young
LLP's report, given on their authority as experts in accounting and auditing.

WHERE YOU CAN FIND MORE INFORMATION

We are a public company and file annual, quarterly and special reports,
proxy statements and other information with the Securities and Exchange
Commission. You may read and copy any document we file at the SEC's Public
Reference Room at 450 Fifth Street, N.W., Washington, D.C. 20549. You can
request copies of these documents by writing to the SEC and paying a fee for the
copying cost. Please call the SEC at 1-800-SEC-0330 for more information about
the operation of the public reference room. Our SEC filings are also available
to the public at the SEC's web site at "http://www.sec.gov." In addition, our
stock is listed for trading on the Nasdaq National Market. You can read and copy
reports and other information concerning us at the offices of the National
Association of Securities Dealers, Inc. located at 1735 K Street, Washington,
D.C. 20006.

This prospectus is only part of a Registration Statement on Form S-3 that
we have filed with the SEC under the Securities Act and therefore omits certain
information contained in the Registration Statement. We have also filed exhibits
and schedules with the Registration Statement that are excluded from this
prospectus, and you should refer to the applicable exhibit or schedule for a
complete description of any statement referring to any contract or other
document. You may:

o inspect a copy of the Registration Statement, including the exhibits
and schedules, without charge at the public reference room or

o obtain a copy from the SEC upon payment of the fees prescribed by the
SEC.

-13-

The SEC allows us to "incorporate by reference" the information we file
with it, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
considered to be a part of this prospectus and information that we file later
with the SEC will automatically update and supersede this information. We
incorporate by reference the documents listed below and any future filings made
with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange
Act of 1934 until the sale of all of the shares of common stock. The documents
we are incorporating by reference are:

o our Quarterly Reports on Form 10-Q for the quarters ended March 31,
2000, June 30, 2000 and September 30, 2000;

o our Annual Report on Form 10-K for the fiscal year ended December 31,
1999;

o the description of our capital stock contained in our Registration
Statement on Form S-1 under the Securities Act as filed with the SEC
on May 13, 1996, including amendments or reports filed for the purpose
of updating that description; and

o the description of Preferred Share Purchase Rights contained in our
Registration Statement on Form 8-A filed with the SEC on February 4,
1999.

You may request a copy of these filings at no cost by writing or
telephoning our Chief Financial Officer at the following address and phone
number:

Microcide Pharmaceuticals, Inc.
850 Maude Avenue
Mountain View, California 94043
(650) 428-1550

-14-

TABLE OF CONTENTS

PAGE
----

PROSPECTUS SUMMARY........................................................... 1

THE COMPANY.................................................................. 1

THE OFFERING................................................................. 1

RISK FACTORS................................................................. 2

FORWARD-LOOKING STATEMENTS................................................... 10

USE OF PROCEEDS.............................................................. 11

PLAN OF DISTRIBUTION......................................................... 12

LEGAL MATTERS................................................................ 13

EXPERTS...................................................................... 13

WHERE YOU CAN FIND MORE INFORMATION.......................................... 13

PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

The table sets forth our estimates (other than the SEC and Nasdaq Filing
Fees) of our expenses in connection with the issuance and distribution of the
common stock being registered. None of the following expenses are being paid by
the holders of options and warrants which may be exercised for such holder's pro
rata portion of the Shares.

ITEM AMOUNT
- ------------------------------------------------- ------

SEC registration fee............................. $ 8,750.00
Legal fees and expenses.......................... $100,000.00
Accounting fees and expenses..................... $ 20,000.00
Miscellaneous fees and expenses.................. $ 21,250.00
Total....................................... $150,000.00

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS.

Section 145 of the General Corporation Law of the State of Delaware
provides that we have the power to indemnify our directors, officers, employees
or agents and certain other persons serving at our request in related capacities
against amounts paid and expenses incurred in connection with an action or
proceeding to which he or she is or is threatened to be made a party by reason
of such position, if such person shall have acted in good faith and in a manner
he reasonably believed to be in or not opposed to our best interests, and, in
any criminal proceeding, if such person had no reasonable cause to believe his
conduct was unlawful, provided that, in the case of actions brought by or on
behalf of us, no indemnification shall be made with respect to any matter as to
which such person shall have been adjudged to be liable to us unless and only to
the extent that the adjudicating court determines that such indemnification is
proper under the circumstances.

Our Restated Certificate of Incorporation provides, as permitted by Section
102(b)(7) of the Delaware General Corporation Law, that directors shall not be
personally liable to us or our stockholders for monetary damages for breach of
fiduciary duty as a director, except for liability: for any breach of a
director's duty of loyalty to us or our stockholders, for acts or omissions not
in good faith or which involve intentional misconduct or knowing violations of
law, under Section 174 of the Delaware General Corporation Law, or for any
transaction from which the director derived an improper personal benefit.

We have a Directors and Officers liability insurance policy that insures
our officers and directors against certain liabilities.

II-1

ITEM 16. EXHIBITS.

EXHIBIT
NUMBER DESCRIPTION
- ------- -------------------------------------------------------------------

4.1 Restated Certificate of Incorporation of the Registrant
(previously filed as Exhibit 3.2 to the Registrant's Registration
Statement on Form S-1, Registration No. 333 - 2400, and
incorporated herein by reference).

5.1 Opinion of Latham & Watkins.*

23.1 Consent of Ernst & Young LLP, Independent Auditors.

23.2 Consent of Latham & Watkins (included in Exhibit 5.1).

24 Power of Attorney (filed in Part II of this Registration Statement).

- ------------
* To be filed by amendment.

ITEM 17. UNDERTAKINGS.

A. RULE 415 OFFERING

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:

(i) To include any prospectus required by Section 10(a)(3) of the
Securities Act;

(ii) To reflect in the prospectus any facts or events arising after
the effective date of the registration statement (or the most recent
post-effective amendment thereof) which, individually or in the aggregate,
represent a fundamental change in the information set forth in the registration
statement. Notwithstanding the foregoing, any increase or decrease in volume of
securities offered (if the total dollar value of securities offered would not
exceed that which was registered) and any deviation from the low or high end of
the estimated maximum offering range may be reflected in the form of prospectus
filed with the Commission pursuant to Rule 424(b) (sec.230.424(b) of this
chapter) if, in the aggregate, the changes in volume and price represent no more
than a 20% change in the maximum aggregate offering price set forth in the
"Calculation of Registration Fee" table in the effective registration statement;
and

(iii) 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 purpose of determining any liability under the
Securities Act, 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.

(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. FILINGS INCORPORATING SUBSEQUENT EXCHANGE ACT DOCUMENTS BY REFERENCE

II-2

The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 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. REGISTRATION STATEMENT PERMITTED BY RULE 430A UNDER THE SECURITIES ACT

(1) For purposes of determining any liability under the Securities Act,
the information omitted from the form of prospectus filed as part of this
registration statement in reliance upon Rule 430A and contained in a form of
prospectus filed by the Registrant pursuant to Rule 424(b)(1) or (4) or 497(h)
under the Securities Act shall be deemed to be part of this registration
statement as of the time it was declared effective.

(2) For the purpose of determining any liability under the Securities Act,
each post-effective amendment that contains a form of prospectus 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.

II-3

SIGNATURES

Pursuant to the requirements of the Securities Act, 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 on Form S-3 to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Mountain View, California, on February 9, 2001.

MICROCIDE PHARMACEUTICALS, INC.

By: /s/ JAMES E. RURKA
-------------------------------------
James E. Rurka
President and Chief Executive Officer

II-4

POWER OF ATTORNEY

KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below constitutes and appoints James E. Rurka his attorney-in-fact, each with
the power of substitution, for him in any and all capacities, to sign any and
all amendments (including post-effective amendments) to this registration
statement, (or any other registration statement for the same offering that is to
be effective upon filing pursuant to Rule 462(b) under the Securities Act) and
to file the same, with all exhibits thereto and other documents in connection
therewith, with the Securities and Exchange Commission, hereby granting unto
said attorneys-in-fact and agents, and each of them, full power and authority to
do and perform each and every act and thing requisite or necessary to be done in
and about the premises, as full to all intents and purposes as he might or could
do in person, hereby ratifying and confirming all that said attorneys-in-fact
and agents or any of them or their or his substitutes may lawfully do or cause
to be done by virtue hereof.

Pursuant to the requirements of the Securities Act, this registration
statement has been signed by the following persons in the capacities and on the
dates indicated.

SIGNATURE TITLE DATE
- -------------------------------- ------------------------------------- ----------------

/s/ JAMES E. RURKA President and Chief Executive Officer February 9, 2001
- -------------------------------- (principal executive officer)
James E. Rurka

/s/ DONALD D. HUFFMAN Vice President, Finance and Corporate February 9, 2001
- -------------------------------- Development (chief financial officer)
Donald D. Huffman

/s/ JOHN P. WALKER Chairman of the Board February 9, 2001
- --------------------------------
John P. Walker

/s/ KEITH A. BOSTIAN, PH.D. Director February 9, 2001
- --------------------------------
Keith A. Bostian, Ph.D.

/s/ DANIEL L. KISNER, M.D. Director February 9, 2001
- --------------------------------
Daniel L. Kisner, M.D.

/s/ HUGH Y. RIENHOFF, JR., M.D. Director February 9, 2001
- --------------------------------
Hugh Y. Rienhoff, Jr., M.D.

/s/ DAVID SCHNELL, M.D. Director February 9, 2001
- --------------------------------
David Schnell, M.D.

Director
- --------------------------------
Mark B. Skaletsky

II-5

MICROCIDE PHARMACEUTICALS

INDEX TO EXHIBITS FILED WITH
FORM S-3 REGISTRATION STATEMENT

EXHIBIT
NUMBER DESCRIPTION
- ------- -------------------------------------------------------------------

5.1 Opinion of Latham & Watkins.*

23.1 Consent of Ernst & Young LLP, Independent Auditors.

23.2 Consent of Latham & Watkins (included in Exhibit 5.1).

24 Power of Attorney (filed in Part II of this Registration Statement).

- ------------
* To be filed by amendment.

II-6