1
                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549

                                    FORM 10-Q

(MARK ONE)

[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

       For the transition period from ________ to ________

       Commission file number 0-19125

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

                Delaware                               33-0336973
     -------------------------------                -------------------
     (State or other jurisdiction of                (I.R.S. Employer 
      incorporation or organization)                Identification No.)

                     2292 Faraday Avenue, Carlsbad, CA 92008
          ------------------------------------------------------------
          (Address of principal executive offices, including zip code)

                                 (760) 931-9200
          ------------------------------------------------------------
              (Registrant's telephone number, including area code)


          ------------------------------------------------------------
              (Former name, former address and former fiscal year,
                         if changed since last report)

    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.

    (1)    Yes  [X] No  [ ]                         (2) Yes  [X]  No [ ]

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

      Common stock $.001 par value                  26,907,483 shares
      ----------------------------           ------------------------------
                 (Class)                     (Outstanding at July 31, 1998)

                    EXHIBIT INDEX: Located at page number 10.


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                           ISIS PHARMACEUTICALS, INC.
                                    FORM 10-Q
                                      INDEX



                                                                                   PAGE
                                                                                   ----
                                                                             
PART I       FINANCIAL INFORMATION

ITEM 1:      Financial Statements

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

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

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

             Notes to Financial Statements                                           6

ITEM 2:      Management's Discussion and Analysis of Financial Condition
             and Results of Operations

             Results of Operations                                                   7

             Liquidity and Capital Resources                                         8

             Year 2000 Computer Issues                                               9

PART II      OTHER INFORMATION

ITEM 1:      Legal Proceedings                                                      10

ITEM 2:      Changes in Securities                                                  10

ITEM 3:      Default upon Senior Securities                                         10

ITEM 4:      Submission of Matters to a Vote of Security Holders                    10

ITEM 5:      Other Information                                                      10

ITEM 6:      Exhibits and Reports on Form 8-K                                       11

SIGNATURES                                                                          12



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                           ISIS PHARMACEUTICALS, INC.
                            CONDENSED BALANCE SHEETS
                        (in thousands, except share data)

                                     ASSETS



                                                                         June 30,       December 31,
                                                                           1998             1997
                                                                        ----------      ------------
                                                                        (Unaudited)        (Note)
                                                                                         
Current assets:
  Cash and cash equivalents                                             $   38,852       $   38,102
  Short-term investments                                                    45,515           48,684
  Prepaid expenses and other current assets                                  2,815            2,364
                                                                        ----------       ----------
          Total current assets                                              87,182           89,150

Property, plant and equipment, net                                          19,787           18,785
Patent costs, net                                                            8,266            7,485
Deposits and other assets                                                    2,400            2,461
                                                                        ----------       ----------
                                                                        $  117,635       $  117,881
                                                                        ==========       ==========

                      LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
  Accounts payable                                                      $    2,746       $    2,843
  Accrued payroll and related expenses                                       1,482            2,242
  Accrued liabilities                                                        4,066            4,347
  Deferred contract  revenues                                               22,558           14,893
  Current portion of long term debt and capital lease                  
  obligations                                                                2,166            2,252
                                                                        ----------       ----------
          Total current liabilities                                         33,018           26,577

Long-term debt and capital lease obligations, less current portion          71,919           56,452

Stockholders' equity:
  Common stock, $.001 par value; 50,000,000 shares
    authorized, 26,855,000 shares and 26,655,000 shares
    issued and outstanding at June 30, 1998 and December 31, 1997,
    respectively                                                                27               27
  Additional paid-in capital                                               191,913          188,793
  Unrealized gain on investments                                               266              165
  Accumulated deficit                                                     (179,508)        (154,133)
                                                                        ----------       ----------
          Total stockholders' equity                                        12,698           34,852
                                                                        ----------       ----------
                                                                        $  117,635       $  117,881
                                                                        ==========       ==========


Note: The balance sheet at December 31, 1997 has been derived from the audited
financial statements at that date.

                             See accompanying notes.


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                           ISIS PHARMACEUTICALS, INC.
                       CONDENSED STATEMENTS OF OPERATIONS
                  (in thousands, except for per share amounts)
                                   (UNAUDITED)



                                         Three months ended               Six  months ended
                                              June 30,                         June 30,
                                       ------------------------        ------------------------
                                         1998            1997            1998            1997
                                       --------        --------        --------        --------
                                                                                
Revenues:
  Research and development
     revenue under collaborative
     agreements                        $  5,832        $  5,793        $ 11,672        $ 10,419
  Interest income                         1,216             766           2,271           1,713
                                       --------        --------        --------        --------
                                          7,048           6,559          13,943          12,132
Expenses:
  Research and development               16,532          13,374          31,391          25,160
  General and administrative              2,261           2,054           4,119           3,761
  Interest expense                        2,102             557           3,806           1,191
                                       --------        --------        --------        --------
                                         20,895          15,985          39,316          30,112
                                       --------        --------        --------        --------
Net loss                               $(13,847)       $ (9,426)       $(25,373)       $(17,980)
                                       ========        ========        ========        ========

Basic and diluted net loss
  per share                            $   (.52)       $   (.36)       $   (.95)       $   (.68)

Shares used in computing basic
  and diluted net loss per share         26,836          26,381          26,788          26,330
                                       ========        ========        ========        ========


                             See accompanying notes.


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                           ISIS PHARMACEUTICALS, INC.
                       CONDENSED STATEMENTS OF CASH FLOWS
                                 (in thousands)
                                   (UNAUDITED)




                                                                          Six months ended
                                                                              June 30,
                                                                      ------------------------
                                                                        1998            1997
                                                                      --------        --------
                                                                                      
Cash used in operations:                                              $(15,112)       $(11,698)

Investing activities:
    Short-term investments                                               3,169           5,797
    Property and equipment                                              (1,881)         (3,856)
    Other assets                                                          (817)         (1,492)
                                                                      --------        --------
            Net cash provided from investing activities                    471             449
                                                                      --------        --------
Financing activities:
    Net proceeds from issuance of common stock                           3,120           1,659
    Proceeds from long-term borrowings                                  13,354          11,378
    Principal payments on debt and capital lease obligations            (1,083)         (3,019)
                                                                      --------        --------
           Net cash provided from  financing activities                 15,391          10,018
                                                                      --------        --------
Net increase (decrease) in cash and cash equivalents                       750          (1,231)

Cash and cash equivalents at beginning of period                        38,102          37,082
                                                                      --------        --------
Cash and cash equivalents at end of period                            $ 38,852        $ 35,851
                                                                      ========        ========

SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION:
    Interest paid                                                     $  1,599        $  1,080

SUPPLEMENTAL DISCLOSURES OF NON-CASH INVESTING AND FINANCING
ACTIVITIES
    Additions to long-term debt obligations for acquisitions of
      property, plant and equipment                                   $    919        $    670


                             See accompanying notes.


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                           ISIS PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS

1.      BASIS OF PRESENTATION

        The unaudited interim financial statements for the three and six month
periods ended June 30, 1998 and 1997 have been prepared on the same basis as the
Company's audited financial statements for the year ended December 31, 1997. The
financial statements include all adjustments (consisting only of normal
recurring adjustments) which the Company considers necessary for a fair
presentation of the financial position at such dates and the operating results
and cash flows for those periods. Results for the interim periods are not
necessarily indicative of the results for the entire year. For more complete
financial information, these financial statements, and notes thereto, should be
read in conjunction with the audited financial statements for the year ended
December 31, 1997 included in the Company's Annual Report on Form 10-K filed
with the Securities and Exchange Commission.

2.       COMPREHENSIVE INCOME

        As of January 1, 1998, the Company adopted Statement of Financial
Accounting Standards No. 130, Reporting Comprehensive Income ("SFAS 130"). This
statement requires the Company to report in the financial statements, in
addition to net income, comprehensive income and its components including
foreign currency translation adjustments and unrealized gains and losses on its
available-for-sale securities. SFAS 130 also requires the Company to reclassify
financial statements for earlier periods provided for comparative purposes. For
the three and six month periods ended June 30, 1998 and 1997 comprehensive
income was not materially different than net income.

3.       SUBSEQUENT EVENT

        In August 1998, the Company entered into an agreement to exclusively
license its issued patents covering immune stimulation by phosphorothioate
oligonucleotides to CpG ImmunoPharmaceuticals, Inc. The agreement grants CpG
ImmunoPharmaceuticals, Inc. exclusive worldwide rights to certain applications
covered by issued U.S. Patents No. 5,663,153; No. 5,723,335; and related patent
applications, not including claims for antisense therapeutics. The terms of the
agreement provide that the Company will receive $5 million in cash payments in
1998. In addition, Isis will receive a 5% equity interest in CpG
ImmunoPharmaceuticals, Inc. Based on recent cash purchases of equity securities
of CpG ImmunoPharmaceuticals, Inc., the value of Isis' equity position will
approximate $1.4 million.


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

        In addition to historical information contained in this Report, this
Report contains forward-looking statements regarding the Company's business and
products and their projected prospects and qualities, and the Company's
relationships with its corporate partners. Such statements are subject to
certain risks and uncertainties, particularly those inherent in both the process
of discovering, developing and commercializing safe and effective drugs, and the
endeavor of building a business around such potential products. Actual results
could differ materially from those projected in this Form 10-Q. As a result, the
reader is cautioned not to place undue reliance on these forward-looking
statements. Factors that could cause or contribute to such differences include,
but are not limited to, those discussed in Isis' Annual Report on Form 10-K for
the year ended December 31, 1997 which is on file with the U.S. Securities and
Exchange Commission, a copy of which is available from the Company.

        Since its inceptions in January 1989, almost all of the Company's
resources have been devoted to its research, drug discovery and drug development
programs. The Company is not yet profitable and expects to continue to have
operating losses for the next several years. Isis' revenue comes from
collaborative research and development agreements with pharmaceutical companies,
research grants and interest income. The revenue from the collaboration
increases the amount of research and development activity that the Company is
able to fund and offsets a portion of its research and development costs. To
date, Isis has not received any significant revenue from the sale of products.

RESULTS OF OPERATIONS

        The Company's revenue from collaborative research and development
agreements was $5.8 million for the second quarter and $11.7 million for the six
month period ended June 30, 1998, compared with $5.8 million and $10.4 million,
respectively, for the same periods in 1997. The revenue increase was primarily
due to the increasing level of development activity supported by our corporate
partners. The Company also had interest income totaling $1.2 million for the
quarter and $2.3 million for the six month period compared with $0.8 million and
$1.7 million for the same periods in 1997. This increase in interest income was
primarily due to higher average investment balances in the quarter ended June
30, 1998.

        Research and development expenses increased to $16.5 million for the
three months and $31.4 million for the six months ended June 30, 1998 from $13.4
million and $25.2 million for the same periods in 1997. This increase was
attributable to an increase in preclinical and clinical development activities
including compounds advancing into more expensive stages of clinical
development. We expect that research and development expenses will continue to
increase as compounds continue to advance in clinical development.

        General and administrative expenses increased to $2.3 million for the
quarter and $4.1 million for the six months ended June 30, 1998, from $2.1
million and $3.8 million for the same periods in 1997. This increase in general
and administrative expense is related to additional staffing in general and
administrative functions required to support the growth in research and
development. We expect that general and administrative expenses will continue to
increase in the future to support our growing research and development efforts.

        Interest expense increased to $2.1 million for the second quarter and
$3.8 million for the six month period ended June 30, 1998, compared with $0.6
million and $1.2 million for the same periods in 1997. This increase in interest
expense is due to borrowing $25 million in a private debt financing completed in
the fourth quarter of 1997 with an additional $15 million follow-on private debt
financing in the second quarter of 1998. Under the terms of these financing
arrangements payment of interest is deferred for the first five years.
Therefore, of the $2.1 million of interest expense recognized in the second
quarter, $1.3 million was accrued under the long-term debt agreements and will
not require current cash payment. Similarly, of the $3.8 million interest
expense for the six-month period ended June 30, 1998, $2.2 million was accrued
under the long-term debt agreements and will not require current cash payment.


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        During the quarter ended June 30, 1998, the Company recorded a net loss
of $13.8 million, or $0.52 per share, compared with $9.4 million, or $0.36 per
share, for the same period in 1997. During the six-month period ended June 30,
1998, the Company's net loss amounted to $25.4 million, or $0.95 per share,
compared to $18.0 million, or $0.68 per share for the same period in 1997. We
expect that operating losses will increase for several more years as research
and development activities grow. Operating losses may fluctuate from quarter to
quarter because of differences in the timing of revenue and expense recognition.

        The Company believes that inflation and changing prices have not had a
material effect on its ongoing operations to date.

LIQUIDITY AND CAPITAL RESOURCES

        Isis has financed its operations with revenue from contract research and
development through the sale of equity securities and the issuance of long-term
debt. From its inception through June 30, 1998, Isis has earned approximately
$117 million in revenue from contract research and development. The Company has
also raised net proceeds of approximately $180 million from the sale of equity
securities since it was founded. Since 1996, Isis has borrowed approximately
$62.6 million under long-term debt arrangements to finance a portion of its
operations.

        As of June 30, 1998, the Company had cash, cash equivalents and
short-term investments totaling $84.4 million and working capital of $54.2
million. In comparison, the Company had cash, cash equivalents and short-term
investments of $86.8 million and working capital of $62.6 million as of December
31, 1997. The decreases in cash and working capital resulted from the funding of
operating losses, investments in capital equipment and principal payments on
debt and capital lease obligations, offset in part, by an additional $15 million
private debt financing.

        The Company's collaborative agreement with Boehringer Ingelheim provides
Isis with a $40 million line of credit. This line of credit is available under
certain circumstances and is to be used to support the collaboration cell
adhesion programs. As of June 30, 1998, the outstanding balance under this line
of credit was $22.6 million.

        In October 1997, Isis borrowed $25 million in a private transaction. The
loan bears interest at 14% per annum and must be repaid on November 1, 2007. No
payments of either principal or interest are required during the first five
years of the loan. After the first five years, interest must be paid quarterly.
No principal payments are required until November 1, 2007. In conjunction with
this transaction, Isis issued warrants to purchase 500,000 shares of common
stock at a price of $25 per share. On May 1, 1998, the Company completed a
follow-on $15 million private debt financing. This financing was a follow-on to
the Company's October 1997 $25 million private debt financing and bears the same
terms and conditions. Because interest is deferred during the first five years,
the combined principal balance of both borrowings will accrue to a total of $78
million on November 1, 2002. In conjunction with this follow-on transaction,
Isis issued warrants to purchase 300,000 shares of common stock at a price of
$25 per share. The warrants issued in connection with both of these financings
expire on November 1, 2004. The debt under these arrangements is carried on the
balance sheet net of the amortized amount allocated to the warrants and
including accrued interest. The combined carrying amount of these notes at June
30, 1998 was $42.4 million.

        The Company had long-term debt and capital lease obligations at June 30,
1998 totaling $71.9 million, versus $56.5 million at December 31, 1997. This
increase was due to the additional follow-on debt financing and the accrual of
interest on the ten-year notes described above, partially offset by principal
repayments on existing obligations. We expect that capital lease obligations
will increase over time to fund capital equipment acquisitions required for the
Company's growing business. We will continue to use lease financing as long as
the terms remain commercially attractive. We believe that the Company's existing
cash, cash equivalents and short-term investments, combined with interest income
and contract revenue will be sufficient to meet its anticipated requirements for
at least two years.


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Year 2000 Computer Issues

        Until recently many computer programs were written to store only 2
digits of date-related information. Thus the programs were unable to distinguish
between the year 1900 and the year 2000. As a result, many computer experts have
significant concerns regarding how those programs will function after December
31, 1999. This is frequently referred to as the "Year 2000 Problem." The Company
is in the process of reviewing its computer systems and other equipment that
utilize embedded microprocessors to assess the potential exposure to this
problem. Because Isis was founded in 1989 and all of its computer systems and
equipment have been purchased or upgraded since that time, we believe the risk
of material disruption to the Company's operations as a result of the presence
of this defect in its own computer systems and equipment is minimal.

        The company has also initiated discussions with its significant
suppliers, corporate partners and financial institutions to ensure that those
parties have appropriate plans to address Year 2000 issues where their systems
could impact Isis' operations. The Company is assessing the extent to which its
operations are vulnerable should those organizations fail to properly modify
their computer systems.

        A team of Isis employees is conducting the Company's Year 2000
initiative. The team's activities are designed to ensure that there is no
adverse effect on the Company's core business operations and that transactions
with customers, suppliers, corporate partners and financial institutions are
fully supported. These efforts are scheduled to be completed by early 1999.
While the Company believes its planning and preparations will be adequate to
address its Year 2000 concerns, there can be no guarantee that the systems of
other companies on which the Company's systems and operations rely will be
converted on a timely basis and will not have a material effect on the Company.
The Company does not yet have a formal contingency plan. A contingency plan will
be finalized as the risk assessment is completed. Based on the information
obtained to date, the cost of identifying and remediating exposures to the Year
2000 Problem is not expected to be material to the Company's results of
operations or financial position.




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ITEM 1. LEGAL PROCEEDINGS

        The Company is not a party to any material legal proceedings.

ITEM 2. CHANGES IN SECURITIES

        Not applicable.

ITEM 3. DEFAULT UPON SENIOR SECURITIES

        Not applicable.

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

        (a) The Company held its Annual Meeting of Stockholders on May 22, 1998.

        (b) Burkhard Blank, M.D., Stanley T. Crooke, M.D. Ph.D. and Mark B.
        Skaletsky were elected to serve as directors for a three-year term and
        until their successors are duly elected and qualified.



                                              Votes in Favor      Votes Withheld
                                              --------------      --------------
                                                                
         Burkhard Blank                         26,104,455            356,894
         Stanley T. Crooke                      26,111,827            356,772
         Mark B. Skaletsky                      26,111,427            357,172


        Other directors whose terms of office continued after the Annual Meeting
        were as follows: Christopher F. O. Gabrieli, Daniel L. Kisner, M.D.,
        Alan C. Mendelson, J.D., William R. Miller, Larry Soll, Ph.D., and
        Joseph H. Wender.

        (c) The following items were approved at the Annual Meeting:

            (1) An increase in the number of shares authorized for issuance
                under the Company's 1998 Stock Option Plan from 8,200,000 to
                10,200,000, the extension of the term of the 1989 Plan until
                January 31, 2008 and the amendment to the stockholder approval
                requirements of the 1989 Plan.


                                                       
                      Votes in favor:                     14,082,001
                      Votes withheld:                      2,411,387
                      Abstentions:                           151,590
                      Unvoted:                             9,823,621


            (2) The selection of Ernst & Young LLP as independent auditors of
                the Company for its fiscal year ending December 31, 1998. 


                                                       
                      Votes in favor:                     26,336,372 
                      Votes withheld:                         68,746 
                      Abstentions:                            63,481


ITEM 5. OTHER INFORMATION

        Pursuant to the Company's bylaws, stockholders who wish to bring matters
        or propose nominees for director at the Company's 1999 annual meeting of
        stockholders must provide specified information to the Company by
        December 14, 1998 (unless such matters are included in the Company's
        proxy statement pursuant to Rule 14a-8 under the Securities Exchange Act
        of 1934, as amended).


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ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

     a. Exhibits

        The following documents are exhibits to this Form 10-Q:

        10.1  First Supplement to Purchase Agreement for 14% Senior Subordinated
              Discount Notes due November 1, 2007 and Warrants for Common Stock
              dated May 1, 1998 (with certain confidential information deleted).

        10.2  Research Collaboration and License Agreement between Merck & Co.,
              Inc. and Isis Pharmaceuticals, Inc. dated June 1, 1998 (with
              certain confidential information deleted).

        27    Financial Data Schedule 

     b. Reports on Form 8-K

        The Company filed no reports on Form 8-K during the quarter ended 
        June 30, 1998.



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                           ISIS PHARMACEUTICALS, INC.

                                   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.

                           ISIS PHARMACEUTICALS, INC.
                                  (Registrant)


Date: August 14, 1998   By: /S/ STANLEY T. CROOKE
                            ----------------------------------------------------
                            Stanley T. Crooke, M.D., Ph.D.
                            Chairman of the Board and Chief Executive Officer
                            (Principal Executive Officer)


Date: August 14, 1998   By: /S/ B. LYNNE PARSHALL
                            ----------------------------------------------------
                            B. Lynne Parshall
                            Executive Vice President and Chief Financial Officer
                            (Principal Financial Officer)


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