UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION

                             Washington, D.C. 20549


                                    FORM 10-Q



(X)      QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
         EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 1998


OR

(  )     TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
         EXCHANGE ACT OF 1934


                         Commission file number: 0-28006


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


           Delaware                                             94-3186021
(State or other jurisdiction of                             (I.R.S. Employer
 incorporation of organization)                           Identification Number)

850 Maude Avenue, Mountain View, California                     94043
 (Address of principal executive offices)                       (ZIP Code)


Registrant's telephone number, including area code:             650-428-1550


Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the  preceding 12 months (or for such shorter period  that  the  registrant  was
required  to file  such  reports),  and  (2) has  been  subject  to such  filing
requirements for the past 90 days.

                                 Yes X      No
                                    ---    ---

Number of shares of Common Stock, no par value, outstanding as of July 31, 1998:
10,971,930.





                         MICROCIDE PHARMACEUTICALS, INC.

                               INDEX FOR FORM 10-Q

                                  JUNE 30, 1998


                                                                           PAGE
                                                                          NUMBER
PART I    FINANCIAL INFORMATION

Item 1.   Financial Statements and Notes

          Condensed Balance Sheets as of June 30, 1998
          and December 31, 1997                                                3

          Condensed Statements of Operations for the three
          and six months ended June 30, 1998 and June 30, 1997                 4

          Condensed Statements of Cash Flows for the six
          months ended June 30, 1998 and June 30, 1997                         5

          Notes to Condensed Financial Statements                              6

Item 2.   Management's Discussion and Analysis of Financial
          Condition and Results of Operations                                  8


PART II   OTHER INFORMATION                                                   11

Item 1.   Legal Proceedings

Item 2.   Changes in Securities

Item 3.   Defaults in Senior Securities

Item 4.   Submission of Matters to a Vote of Security Holders

Item 5.   Other Information

Item 6.   Exhibits and Reports on Form 8-K


SIGNATURES                                                                   13

                                       -2-




                         MICROCIDE PHARMACEUTICALS, INC.

                            CONDENSED BALANCE SHEETS
                                 (In thousands)


                                                          June 30,  December 31,
                                                             1998        1997
                                                           --------    --------
                                                         (Unaudited)
ASSETS
     Current assets:
          Cash and cash equivalents                        $  2,890    $ 11,763
          Short-term investments                             31,024      28,624
          Prepaid expenses and other current assets           1,925       1,284
                                                           --------    --------
     Total current assets                                    35,839      41,671
                                                           --------    --------

          Property and equipment, net                         9,780       9,540
          Other assets                                          885         571
                                                           --------    --------

Total assets                                               $ 46,504    $ 51,782
                                                           ========    ========


LIABILITIES AND STOCKHOLDERS' EQUITY
     Current liabilities:
          Accounts payable                                 $    990    $  1,313
          Construction payable                                  344         347
          Accrued compensation                                  779         746
          Current portion of capital lease obligations          377         612
          Deferred revenue                                      875         786
          Other accrued liabilities                             675         632
                                                           --------    --------
     Total current liabilities                                4,040       4,436
                                                           --------    --------

     Long-term portion of capital lease obligations              82         224
     Accrued rent                                               164         226


Stockholders' equity:
     Common stock                                            66,792      66,930
     Deferred compensation                                     (725)     (1,251)
     Net unrealized loss on marketable securities               (58)        (44)
     Accumulated deficit                                    (23,791)    (18,739)
                                                           --------    --------
Total stockholders' equity                                   42,218      46,896
                                                           --------    --------

Total liabilities & stockholders' equity                   $ 46,504    $ 51,782
                                                           ========    ========


NOTE:  The balance  sheet at December 31, 1997 has been derived from the audited
financial  statements  at that date but does not include all of the  information
and footnotes required by generally accepted accounting  principles for complete
financial statements.

                  See Notes to Condensed Financial Statements.

                                      -3-





                                                   Microcide Pharmaceuticals, Inc.

                                                 Condensed Statements of Operations
                                              (In thousands, except per share amounts)
                                                             (Unaudited)


                                                                            Three Months Ended               Six Months Ended
                                                                                 June 30,                         June 30,
                                                                        -------------------------         -------------------------
                                                                          1998             1997             1998             1997
                                                                        --------         --------         --------         --------
                                                                                                                    
Revenues
     License and milestone fees                                         $   --           $   --           $   --           $  1,000
     Research revenue                                                      2,800            2,994            5,835            6,101
                                                                        --------         --------         --------         --------

Total revenues                                                             2,800            2,994            5,835            7,101

Operating expenses
     Research and development                                              4,815            4,336            9,876            8,437
     General and administrative                                              953            1,099            2,011            2,121
                                                                        --------         --------         --------         --------

Total operating expenses                                                   5,768            5,435           11,887           10,558
                                                                        --------         --------         --------         --------


Loss from operations                                                      (2,968)          (2,441)          (6,052)          (3,457)

Interest income                                                              504              650            1,030            1,338
Interest expense                                                             (12)             (40)             (30)             (93)
                                                                        --------         --------         --------         --------
Net loss                                                                $ (2,476)        $ (1,831)        $ (5,052)        $ (2,212)
                                                                        ========         ========         ========         ========

Net loss per share                                                      $  (0.23)        $  (0.17)        $  (0.46)        $  (0.21)
                                                                        ========         ========         ========         ========


Shares used in calculation of net loss per share                          10,957           10,778           10,941           10,797

<FN>
                                            See Notes to Condensed Financial Statements.
</FN>


                                                                -4-





                                                   Microcide Pharmaceuticals, Inc.

                                                 CONDENSED STATEMENTS OF CASH FLOWS
                                          Increase (decrease) in cash and cash equivalents



                                                                                                            Six Months Ended
                                                                                                                 June 30
                                                                                                      -----------------------------
                                                                                                        1998                 1997
                                                                                                      --------             --------
                                                                                                                           
Cash flows used in operating activities:
     Net loss                                                                                         $ (5,052)            $ (2,212)
     Adjustments to reconcile net loss to net cash provided by
     (used in) operating activities:
          Depreciation and amortization                                                                  1,466                1,258
          Amortization of deferred compensation                                                            264                  295
          Accrued rent                                                                                     (62)                  32
          Net unrealized gain (loss) on securities                                                         (14)                  25
     Changes in assets and liabilities:
          Prepaid expenses and other current assets                                                       (641)                (235)
          Other assets                                                                                    (314)                   6
          Accounts payable                                                                                (326)              (1,355)
          Accrued compensation and other accrued liabilities                                                76                  389
          Deferred revenue                                                                                  89                  125
                                                                                                      --------             --------

Net cash used in operating activities                                                                   (4,514)              (1,672)
                                                                                                      --------             --------

Cash flows used in investing activities:
     Purchase of short-term investments                                                                (26,410)             (62,015)
     Maturities of short-term investments                                                               24,010               61,290
     Capital expenditures                                                                               (1,708)              (1,308)
                                                                                                      --------             --------

Net cash provided by (used in) investing activities                                                     (4,108)              (2,033)
                                                                                                      --------             --------

Cash flows financing activities:
     Principal payments on capital lease obligations                                                      (377)                (582)
     Repayment of shareholder note                                                                           0                   35
     Net proceeds from issuance of common stock                                                            126                  126
                                                                                                      --------             --------

Net cash used in financing activities                                                                     (251)                (421)
                                                                                                      --------             --------

Net decrease in cash and cash equivalents                                                               (8,873)              (4,126)
Cash and cash equivalents at beginning of period                                                        11,763                8,317
                                                                                                      --------             --------

Cash and cash equivalents at end of period                                                            $  2,890             $  4,191
                                                                                                      ========             ========

Supplemental disclosure of cash flow information:
     Income taxes paid                                                                                $      2             $     21
                                                                                                      ========             ========
     Interest paid                                                                                    $     30             $     81
                                                                                                      ========             ========

<FN>
                                            See Notes to Condensed Financial Statements.
</FN>


                                                                -5-



                         MICROCIDE PHARMACEUTICALS, INC.

                     NOTES TO CONDENSED FINANCIAL STATEMENTS

                                  June 30, 1998
                                   (Unaudited)


1.  Summary of Significant Accounting Policies
     Organization and Basis of Presentation

         Microcide Pharmaceuticals,  Inc. (the "Company") 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. The Company's discovery and development programs address the growing
problem of bacterial drug  resistance  and the need for improved  antifungal and
antiviral agents through two principal themes: (i) Targeted  Antibiotics,  which
focuses on developing novel antibiotics and antibiotic  potentiators to directly
address existing  bacterial  resistance  problems,  and (ii) Targeted  Genomics,
which utilizes  bacterial,  fungal and viral genetics to discover new classes of
antimicrobials and other novel treatments for infectious diseases.

         The accompanying  unaudited  condensed  financial  statements have been
prepared in accordance with generally accepted accounting principles for interim
financial  information and with the  instructions to Form 10-Q and Rule 10-01 of
Regulation  S-X.  Accordingly,  they do not include all of the  information  and
footnotes  required by generally  accepted  accounting  principles  for complete
financial statements. In the opinion of management,  all adjustments (consisting
of normal recurring accruals)  considered necessary for a fair presentation have
been included.  The results of operations  for the interim  periods shown herein
are not necessarily indicative of operating results for the entire year.

         This unaudited  financial  data should be read in conjunction  with the
financial  statements and footnotes  contained in the Company's annual report on
Form 10-K for the year ended December 31, 1997.

2.  Investments

         Investment securities are classified as  available-for-sale  (estimated
fair value) and consist of the following investments (in thousands):

                                                     June 30,       December 31,
                                                       1998             1997
                                                     -------           -------
Cash equivalents and short-term investments:                        
         Money market funds                          $ 4,588           $ 2,133
         Corporate debt securities                    26,436            37,417
                                                     -------           -------
                                                     $31,024           $39,550
                                                     =======           =======
                                                                    
                                       -6-





3.  Per Share Information

         Effective December 31, 1997, the Company adopted statement of Financial
Accounting  Standards  No. 128  "Earnings  per  Share"  ("SFAS  128").  SFAS 128
requires  the  presentation  of basic  earnings  (loss)  per share  and  diluted
earnings  (loss) per share,  if more  dilutive,  for all periods  presented.  In
accordance  with SFAS 128,  basic net loss per share has been computed using the
weighted-average number of shares of Common Stock outstanding during the period.
Diluted net loss per share has not been presented;  given the Company's net loss
position, the result would be anti-dilutive.

4. Changes in Accounting Standards

         As of January 31,  1998,  the Company  adopted  Statement  of Financial
Accounting Standards No. 130 "Reporting Comprehensive Income" ("SFAS 130"). SFAS
130 established new rules for the reporting and display of comprehensive  income
and its components; however, the adoption of this Statement has no impact on the
Company's  net loss or  stockholders'  equity.  SFAS 130  requires,  among other
things, unrealized gains or losses on the Company's securities to be included in
comprehensive  income or loss.  During  the six months  ended June 30,  1998 and
1997, the Company's  comprehensive  loss amounted to $5,066,000 and  $2,187,000,
respectively.


                                      -7-





                         MICROCIDE PHARMACEUTICALS, INC.

         Management's Discussion and Analysis of Financial Condition and
                              Results of Operations

Overview

         As  part  of  the  Company's  strategy  to  enhance  its  research  and
development  capabilities  and to  fund,  in  part,  its  capital  requirements,
Microcide   has  entered  into   collaborative   agreements   with  three  major
pharmaceutical  companies.  The  Company has  received  license  fees,  research
support  payments and milestone  payments  pursuant to these  agreements and can
potentially receive additional research support payments,  additional  milestone
payments and royalty  payments.  License  payments are  typically  nonrefundable
up-front payments for licenses to develop,  manufacture and market products,  if
any,  that are  developed  as a result of the  collaboration.  Research  support
payments are  typically  contractually  obligated  payments to fund research and
development over the term of the collaboration.  Milestone payments are payments
contingent  upon the achievement of specified  milestones,  such as selection of
candidates for drug development,  the commencement of clinical trials or receipt
of regulatory approvals.  If drugs are successfully developed and commercialized
as a result of the  collaborative  agreements,  the Company will receive royalty
payments based upon the net sales of such drugs.

         Through June 30, 1998, the Company had received in the aggregate  $35.0
million in license fees,  milestone payments and research support payments under
the  collaborative  agreements.  Assuming  none  of the  existing  collaborative
agreements is terminated prior to its scheduled expiration,  the Company will be
entitled  to receive up to an  additional  $16.0  million  of  research  support
payments. In addition, in the event that any of the collaborative agreements are
extended  beyond their  current  terms,  the Company will be entitled to receive
additional research support payments.

         In the event that the  Company  achieves  the  specified  research  and
product  development  milestones,  the  Company  will  be  entitled  to  receive
milestone  payments  under its  collaborative  agreements  with the three  major
pharmaceutical  companies  ranging  from  $13.0  million  to $32.5  million  per
product.  No royalty  payments  have yet been  received and the Company does not
expect to receive  royalties based upon the net sales of drugs for a significant
number of years, if ever.

         In May  1998,  the  Company  signed  an  agreement  to  extend  various
facilities  leases for a 60-month  term after their  scheduled  expiration.  The
lease combines other  previous  agreements  signed in relation to its facilities
comprising  71,210 square feet.  The agreement  calls for total minimum  monthly
rental payments ranging from $132,000 to $152,000 beginning on October 1, 2000.

         Quarterly results of operations are subject to significant fluctuations
based  on  the  timing  and  amount  of  certain   revenues   earned  under  the
collaborative  agreements.  The Company expects to incur operating losses in the
future.

         This Form 10-Q contains  forward-looking  statements based upon current
expectations,  including  statements  with  regard to the  potential  receipt of
additional research support payments,  milestone payments and royalties from the
Company's  collaborative partners, and the period of time the Company's existing
capital  resources and future  payments under  collaborative  agreements will be
sufficient  to  satisfy  the  Company's   funding   requirements,   expectations
concerning  the  Company's  


                                      -8-


future  research and  development  and general and  administrative  expenses and
future  facility  needs.  Such  forward-looking   statements  involve  risk  and
uncertainties,  including  without  limitation,  the  risk  that  the  Company's
collaborations   will  be  terminated,   development   candidates  will  not  be
identified,  development  candidates which are selected will not proceed through
pre-clinical trials or will not prove safe and effective for treatment of humans
in clinical trials, or that the  identification,  selection,  pre-clinical,  and
clinical testing of development  candidates will take substantially longer or be
substantially  more  expensive  than  contemplated  by the Company,  or that the
Company  will not be able to  obtain  on a timely  basis  government  regulatory
clearance  required for clinical  testing,  manufacturing,  and marketing of its
products,  and the other  risks  and  uncertainties  set forth in the  Company's
annual report on Form 10-K for the year ended December 31, 1997.  Actual results
and timing of certain events could differ materially from those indicated in the
forward-looking statements as a result of these or other factors.

Results of Operations

Three Months Ended June 30, 1998 and 1997

Revenues.  Total  revenues for the second  quarter of 1998 were $2.8 million,  a
decrease  of 6% from the $3.0  million  in  revenues  recognized  in the  second
quarter of 1997,  due to a  decrease  in  research  support  revenues.  Research
support  revenue  decreased in the second quarter of 1998 due primarily to lower
revenues  earned  from the  Daiichi  collaborative  agreement  resulting  from a
decrease  in  reimbursable  costs  associated  with the  program.  There were no
license and milestone fees earned for either period.

Research and Development  Expenses.  Research and  development  expenses for the
second  quarter  increased  approximately  11% from $4.3 million in 1997 to $4.8
million in 1998.  The  increases are due  primarily to higher  compensation  and
other  employee-related  expenses  associated  with an increase in  headcount to
support the Company's corporate collaborations and its internal programs, higher
spending for research supplies and materials,  higher costs relating to expanded
research  and  development  facilities,  and  costs  associated  with  providing
research  support  to  Iconix  Pharmaceuticals  related  to the  viral  research
program,  partially offset by lower expenses related to assembling the Company's
molecular diversity  collection.  Research and development expenses are expected
to further increase in the third quarter.

General and Administrative Expenses. General and administrative expenses for the
second quarter  decreased 13% from $1.1 million in 1997 to $1.0 million in 1998.
Decreased  expenses primarily  consisted of lower operational costs,  travel and
entertainment costs, and facilities costs.  General and administrative  expenses
may increase in dollar amounts in the third quarter, but are expected to be at a
lower percentage of total operating expenses.

Interest Income and Expense.  Interest  income for the second quarter  decreased
from  $650,000  in 1997 to  $504,000  in 1998,  primarily  due to a decrease  in
average cash balances.  Interest  expense for the second quarter  decreased from
$40,000 in 1997 to $12,000 in 1998 due to a decrease in capital  lease  balances
outstanding.

Six Months Ended June 30, 1998 and 1997

Revenues.  Total  revenues  for the  first  half of 1998 were  $5.8  million,  a
decrease  of 18% from the $7.1  million in  revenues  for the first half of 1997
primarily due to a decrease in license and



                                      -9-


milestone  fees.  In addition,  research  support  revenue  decreased  from $6.1
million  in the first  half of 1997 to $5.8  million  in the first  half of 1998
primarily as a result of lower  revenues  earned from the Daiichi  collaborative
agreement  resulting from a decrease in reimbursable  costs  associated with the
program.

Research and Development  Expenses.  Research and  development  expenses for the
first half of 1998 were $9.9 million, an increase of approximately 17% from $8.4
million in the first half of 1997,  primarily due to increased  compensation and
other  employee-related  expenses  associated  with an increase in  headcount to
support the Company's corporate collaborations and its internal programs, higher
spending for research supplies and materials,  higher costs relating to expanded
research  and  development  facilities,  and  costs  associated  with  providing
research  support  to  Iconix  Pharmaceuticals  related  to the  viral  research
program,  partially offset by lower expenses related to assembling the Company's
molecular diversity  collection.  Research and development expenses are expected
to further increase in the second half of 1998.

General and Administrative Expenses. General and administrative expenses for the
first half of 1998 decreased  approximately 5% from $2.1 million in 1997 to $2.0
million in 1998.  Decreased  expenses  primarily  consisted of lower payroll and
related expenses,  lower  operational  costs, and lower travel and entertainment
costs,  partially offset by an increase in outside service  expenses  associated
with  recruiting,  legal and insurance  activities.  General and  administrative
expenses may  increase in dollar  amounts in the second half of 1998 as compared
to the first half of 1998, but are expected to be at a lower percentage of total
operating expenses.

Interest  Income  and  Expense.  Interest  income  for  the  first  half of 1998
decreased from $1.3 million in 1997 to $1.0 million in 1998,  primarily due to a
decrease in average cash balances.  Interest  expense  decreased from $93,000 in
the first half of 1997 to $30,000 in the first half of 1998 due to a decrease in
capital lease balances outstanding.

Liquidity and Capital Resources

         The Company has  financed  its  operations  since  inception  primarily
through  the  sale  of  equity,   through  funds  provided  under  collaborative
agreements,  through other revenues principally consisting of sales of molecular
diversity  samples  and  through  equipment  financing.  As of June 30, 1998 the
Company had received  approximately  $64.5 million in net proceeds from the sale
of equity and  approximately  $36.7  million  from license and  milestone  fees,
research support payments under collaborative  agreements and sales of molecular
diversity samples.

         Cash, cash equivalents and short-term investments at June 30, 1998 were
$33.9  million  compared to $40.4  million at December  31,  1997.  The decrease
during the first half of 1998 was due  primarily to cash used by  operations  of
$4.5  million,  $1.7 million in capital  expenditures  and $251,000  utilized in
financing  activities  which  predominantly  consisted of principal  payments on
capital lease obligations.

         The Company  believes  that its existing  capital  resources,  interest
income and future  payments due under  collaborative  agreements will enable the
Company to maintain current and planned operations at least through 1999.


                                      -10-



PART II      OTHER INFORMATION

Item 1.      Legal Proceedings

             None.

Item 2.      Changes in Securities

             None.

Item 3.      Defaults in Senior Securities

             None.

Item 4.      Submission of Matters to a Vote of Security Holders

       (a)   The Annual Meeting of  Stockholders  of Microcide  Pharmaceuticals,
             Inc. was held on June 18, 1998.


       (b)   The following  Class II Directors  were elected to serve for a term
             of three years to expire at the  Company's  2001 Annual  Meeting of
             Stockholders:


             Name                                    Position                            Term Expires
             ----------------------------------      ---------------------------------   ------------
                                                                                         
             Hugh Y. Rienhoff, Jr., M.D.             Class II Director                        2001
             John P. Walker                          Class II Director                        2001



             The  following  Class I and III  Directors  continue to serve their
             respective  terms which expire at the Company's  Annual  Meeting of
             Stockholders in the year as noted:


             Name                                    Position                            Term Expires
             ----------------------------------      ---------------------------------   ------------
                                                                                         
             Daniel L. Kisner, M.D.                  Class I Director                         2000
             David Schnell, M.D.                     Class I Director                         2000
             Mark B. Skaletsky                       Class I Director                         2000
             Keith A. Bostian, Ph.D.                 Class III Director                       1999
             James E. Rurka                          Class III Director                       1999


       (c)   The matters  voted upon at the meeting and the voting  results were
             as follows:


             (i)   The  election of two Class II  Directors  for a term of three
                   years:


             Name                                          For                  Against    Abstain  Not Voted
             ---------------------------                ---------               -------    -------  ---------
                                                                                        
             Hugh Y. Rienhoff, Jr., M.D.                8,582,585               128,973       -     2,226,934
             John P. Walker                             8,592,285               119,273       -     2,226,934





                                      -11-






             (ii)  Approval of amendment to the Company's 1993 Amended Incentive
                   Stock Plan,  increasing  the number of shares of Common Stock
                   reserved for issuance from 1,880,000 to 2,280,000:

                        For                      Against                   Abstain               Not Voted
                     ---------                   -------                   ------                ---------
                                                                                              
                     8,141,242                   547,396                   22,920                2,226,934



             (iii) Ratification  of the  appointment  of  Ernst &  Young  LLP as
                   independent  auditors for the fiscal year ending December 31,
                   1998:


                        For                      Against                   Abstain               Not Voted
                     ---------                   -------                   ------                ---------
                                                                                              
                     8,686,515                    13,284                    11,759               2,226,934


Item 5.      Other Information

             None.

Item 6.      Exhibits and Reports on Form 8-K

     (a)     The following exhibits have been filed with this report:

             10.22  Lease agreement between the Registrant and Portola Land Co. 
                    dated May 1998
             27.1   Financial Data Schedule

     (b)     Reports on Form 8-K.
             No reports on Form 8-K were filed during the quarter ended June 30,
             1998.




                                      -12-






                                   SIGNATURES




         Pursuant to the  requirements  of the Securities  Exchange Act of 1934,
the  registrant  has duly  caused  this report to be signed on its behalf by the
undersigned, thereunto duly authorized.


Dated:   August 14, 1998




                                MICROCIDE PHARMACEUTICALS, INC.
                                ------------------------------------------------
                                (Registrant)


                                /s/ James E. Rurka
                                ------------------------------------------------
                                President, Chief Executive Officer and Director
                                (principal executive officer)



                                /s/ Matthew J. Hogan
                                ------------------------------------------------
                                Chief Financial Officer
                                (principal financial and accounting officer)




                                      -13-