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


                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

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

                                    FORM 10-Q


[x]   Quarterly report pursuant to Section 13 or 15(d) of the Securities and
      Exchange Act of 1934 For the quarterly period ended June 30, 1999
                                       OR
[ ]   Transition report pursuant to Section 13 or 15(d) of the Securities and
      Exchange Act of 1934 For the transition period from _______ to _________


                        Commission File Number 000-19319

                       VERTEX PHARMACEUTICALS INCORPORATED
             (Exact name of registrant as specified in its charter)


          Massachusetts                                          04-3039129
          -------------                                          ----------
(State or other jurisdiction of                               (I.R.S. Employer
incorporation or organization)                               Identification No.)


             130 Waverly Street, Cambridge, Massachusetts 02139-4242
             -------------------------------------------------------
          (Address of principal executive offices, including zip code)

                                 (617) 577-6000
                                 --------------
              (Registrant's telephone number, including area code)


         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
                                   -----   -----


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

Common Stock, Par Value $.01 Per Share                     25,534,912
- --------------------------------------            ----------------------------
               Class                              Outstanding at August 4, 1999

                                      -1-




                       VERTEX PHARMACEUTICALS INCORPORATED

                                      INDEX





                                                                                                     Page
                                                                                                     ----
                                                                                                   

PART I. -  FINANCIAL INFORMATION
      Item 1.   Condensed Consolidated Financial Statements

                  Report of Independent Accountants                                                    3

                  Condensed Consolidated Balance Sheets -
                           June 30, 1999 and December 31, 1998                                         4

                  Condensed Consolidated Statements of Operations -
                           Three Months Ended June 30, 1999 and 1998                                   5

                  Condensed Consolidated Statements of Operations -
                           Six Months Ended June 30, 1999 and 1998                                     6

                  Condensed Consolidated Statements of Cash Flows -
                           Six Months Ended June 30, 1999 and 1998                                     7

                  Notes to Condensed Consolidated Financial Statements                                 8

      Item 2.   Management's Discussion and Analysis of Financial
                           Condition and Results of Operations                                        10


PART II. -  OTHER INFORMATION                                                                         14

SIGNATURES                                                                                            15



                                      -2-



                        REPORT OF INDEPENDENT ACCOUNTANTS

To the Board of Directors and Shareholders of Vertex Pharmaceuticals
Incorporated:

We have reviewed the accompanying condensed consolidated balance sheet of
Vertex Pharmaceuticals Incorporated as of June 30, 1999, and the related
condensed consolidated statements of operations for each of the three-month
and six-month periods ended June 30, 1999 and 1998 and the condensed
consolidated statements of cash flows for the six-month periods ended June
30, 1999 and 1998. These financial statements are the responsibility of the
company's management.

We conducted our review in accordance with standards established by the American
Institute of Certified Public Accountants. A review of interim financial
information consists principally of applying analytical procedures to financial
data and making inquiries of persons responsible for financial and accounting
matters. It is substantially less in scope than an audit conducted in accordance
with generally accepted auditing standards, the objective of which is the
expression of an opinion regarding the financial statements taken as a whole.
Accordingly, we do not express such an opinion.

Based on our review, we are not aware of any material modifications that should
be made to the accompanying condensed consolidated interim financial statements
for them to be in conformity with generally accepted accounting principles.

We have previously audited in accordance with generally accepted auditing
standards, the consolidated balance sheet as of December 31, 1998, and the
related consolidated statements of operations, stockholders' equity, and cash
flows for the year then ended (not presented herein); and in our report dated
February 25, 1999, we expressed an unqualified opinion on those consolidated
financial statements. In our opinion, the information set forth in the
accompanying condensed consolidated balance sheet as of December 31, 1998, is
fairly stated, in all material respects, in relation to the consolidated
balance sheet from which it has been derived.

PricewaterhouseCoopers LLP

Boston, Massachusetts
July  27, 1999


                                      -3-



                       VERTEX PHARMACEUTICALS INCORPORATED

                      CONDENSED CONSOLIDATED BALANCE SHEETS

                                 (In thousands)
                                   (Unaudited)




                                                                        June 30,             December 31,
                                                                          1999                    1998
                                                                          ----                    ----
                                                                                          


                                     ASSETS

Current assets:
     Cash and cash equivalents                                          $ 11,173                $  24,169
     Short-term investments                                              193,819                  221,483
     Prepaid expenses and other current assets                             6,342                    3,056
                                                                       ---------                ---------

           Total current assets                                          211,334                  248,708

Restricted cash                                                            4,198                    2,316
Property and equipment, net                                               19,658                   14,476
Investment in equity affiliate                                             2,575                      ---
Other assets                                                                 867                      846
                                                                       ---------                ---------

           Total assets                                                $ 238,632                $ 266,346
                                                                       ---------                ---------
                                                                       ---------                ---------


                      LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Obligations under capital lease and debt                          $   2,561                $   2,752
     Accounts payable and accrued expenses                                11,659                   10,350
                                                                       ---------                ---------

           Total current liabilities                                      14,220                   13,102
                                                                       ---------                ---------

Obligations under capital leases and debt,
     excluding current portion                                             5,828                    7,032
                                                                       ---------                ---------

           Total liabilities                                              20,048                   20,134
                                                                       ---------                ---------

Stockholders' equity:
     Preferred stock, $.01 par value; 1,000,000 shares authorized;
       none issued
     Common stock, $0.1 par value; 100,000,000 shares authorized;
       issued and outstanding--25,508,028 shares in 1999
       and 25,358,559 in 1998                                                255                      254
     Additional paid-in capital                                          397,518                  395,165
     Accumulated other comprehensive income                                 (933)                     654
     Accumulated deficit                                                (178,256)                (149,861)
                                                                       ---------                ---------

                  Total stockholders' equity                             218,584                  246,212
                                                                       ---------                ---------
           Total liabilities and stockholders' equity                  $ 238,632                $ 266,346
                                                                       ---------                ---------
                                                                       ---------                ---------



                 The accompanying notes are an integral part of
               these condensed consolidated financial statements.


                                      -4-



                       VERTEX PHARMACEUTICALS INCORPORATED

                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (Unaudited)
                    (In thousands, except per share amounts)




                                                        Three Months Ended June 30,
                                                        ---------------------------
                                                              1999          1998
                                                          --------      --------
                                                                  

Revenues:
     Royalties and product sales                          $  2,874          --
     Collaborative and other research and development        9,642      $  3,247
     Investment income                                       2,812         3,905
                                                          --------      --------

           Total revenues                                   15,328         7,152
                                                          --------      --------

Costs and expenses:
     Royalties and product costs                             1,199          --
     Research and development                               19,029        12,631
     General and administrative                              5,466         4,164
     Loss in equity affiliate                                  303          --
     Interest                                                  172           159
                                                          --------      --------

           Total costs and expenses                         26,169        16,954
                                                          --------      --------

Net loss                                                  $(10,841)     $ (9,802)
                                                          --------      --------
                                                          --------      --------

Basic and diluted net loss per common share               $  (0.43)     $  (0.39)
                                                          --------      --------
                                                          --------      --------

Basic and diluted weighted average number of
     common shares outstanding                              25,480        25,289
                                                          --------      --------
                                                          --------      --------




                 The accompanying notes are an integral part of
               these condensed consolidated financial statements.


                                      -5-



                       VERTEX PHARMACEUTICALS INCORPORATED

                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (Unaudited)
                    (In thousands, except per share amounts)




                                                                                    Six Months Ended June 30,
                                                                                    -------------------------
                                                                                       1999          1998
                                                                                     --------      --------
                                                                                             

Revenues:
     Royalties and product sales                                                     $  2,874          --
     Collaborative and other research and development                                  13,605      $  6,420
     Investment income                                                                  5,978         7,901
                                                                                     --------      --------

           Total revenues                                                              22,457        14,321
                                                                                     --------      --------

Costs and expenses:
     Royalties and product costs                                                        1,199          --
     Research and development                                                          37,634        24,813
     General and administrative                                                        11,238         7,417
     Loss in equity affiliate                                                             425          --
     Interest                                                                             356           307
                                                                                     --------      --------

           Total costs and expenses                                                    50,852        32,537
                                                                                     --------      --------

Net loss                                                                             $(28,395)     $(18,216)
                                                                                     --------      --------
                                                                                     --------      --------

Basic and diluted net loss per common share                                          $  (1.12)     $  (0.72)
                                                                                     --------      --------
                                                                                     --------      --------

Basic and diluted weighted average number of
     common shares outstanding                                                         25,434        25,270
                                                                                     --------      --------
                                                                                     --------      --------




                 The accompanying notes are an integral part of
               these condensed consolidated financial statements.


                                      -6-



                       VERTEX PHARMACEUTICALS INCORPORATED

                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (Unaudited)
                                 (In thousands)





                                                         Six Months Ended June 30,
                                                         -------------------------

                                                            1999           1998
                                                         ---------      ---------
                                                                  
Cash flows from operating activities:
     Net loss                                            $ (28,395)     $ (18,216)
     Adjustment to reconcile net loss to
         net cash used by operating activities:
           Depreciation and amortization                     2,649          1,975
           Realized (gains)/losses on short-term
               investments                                    (193)            96
           Loss in equity affiliate                            425           --
     Changes in assets and liabilities:
           Prepaid expenses and other
                current assets                              (3,286)           164
           Accounts payable and accrued
                expenses                                     1,309         (4,634)
           Deferred revenue                                   --             (556)
                                                         ---------      ---------
                Net cash used by
                    operating activities                   (27,491)       (21,171)
                                                         ---------      ---------

Cash flows from investing activities:
     Purchases of investments                             (240,944)      (318,394)
     Sales and maturities of investments                   267,321        306,739
     Expenditures for property and equipment                (7,831)        (4,497)
     Restricted cash                                        (1,882)          --
     Investment in equity affiliate                         (3,000)          --
     Other assets                                              (21)          (471)
                                                         ---------      ---------
           Net cash provided (used) by
                investing activities                        13,643        (16,623)
                                                         ---------      ---------

Cash flows from financing activities:
     Repayment of capital lease obligations and debt        (1,395)        (1,363)
     Proceeds from debt                                       --            2,511
     Proceeds from other issuances of common stock           2,354          1,466
                                                         ---------      ---------
           Net cash provided by
                financing activities                           959          2,614
                                                         ---------      ---------

Effect of exchange rate changes on cash                       (107)          --
                                                         ---------      ---------

Decrease in cash and cash equivalents                      (12,996)       (35,180)

Cash and cash equivalents at beginning of period            24,169         71,454
                                                         ---------      ---------

Cash and cash equivalents at end of period               $  11,173      $  36,274
                                                         ---------      ---------
                                                         ---------      ---------




                 The accompanying notes are an integral part of
               these condensed consolidated financial statements.


                                      -7-




                       VERTEX PHARMACEUTICALS INCORPORATED

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS


1.       BASIS OF PRESENTATION

         The accompanying condensed consolidated financial statements are
unaudited and have been prepared by the Company in accordance with generally
accepted accounting principles.

         Certain information and footnote disclosures normally included in the
Company's annual financial statements have been condensed or omitted. Certain
prior year amounts have been reclassified to conform with current year
presentation. The interim financial statements, in the opinion of management,
reflect all adjustments (including normal recurring accruals) necessary for a
fair statement of the results for the interim periods ended June 30, 1999 and
1998.

         The results of operations for the interim periods are not necessarily
indicative of the results of operations to be expected for the fiscal year,
although the Company expects to incur a substantial loss for the year ended
December 31, 1999. These interim financial statements should be read in
conjunction with the audited financial statements for the year ended December
31, 1998, which are contained in the Company's 1998 Annual Report to its
shareholders and in its Form 10-K filed with the Securities and Exchange
Commission.


2.       ACCOUNTING POLICIES

REVENUE RECOGNITION

         Revenue under research and development arrangements is recognized as
earned under the terms of the respective agreements. License payments are
recorded as revenue when contractual obligations have been met. Product research
funding is recorded as revenue, generally on a quarterly basis, as research
effort is incurred. Deferred revenue arises from payments received which have
not yet been earned under research and development arrangements. The Company
recognizes milestone payments when the milestones are achieved. Royalty revenue
is recognized based on actual and estimated sales of licensed products in
licensed territories. Product sales revenue is recorded upon shipment.

BASIC AND DILUTED LOSS PER COMMON SHARE

         Basic earnings per share is based upon the weighted average number of
common shares outstanding during the period. Diluted earnings per share is based
upon the weighted average number of common shares outstanding during the period
plus additional weighted average common equivalent shares outstanding during the
period when the effect is not anti-dilutive. Common equivalent shares result
from the assumed exercise of outstanding stock options, the proceeds of which
are then assumed to have been used to repurchase outstanding stock using the
treasury stock method. Common equivalent shares have not been included in the
per share calculations as the effect would be anti-dilutive. Total potential
common equivalent shares consist of 5,831,328 stock options outstanding with a
weighted average exercise price of $22.78 as of June 30, 1999.


                                      -8-



                       VERTEX PHARMACEUTICALS INCORPORATED

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

3.       COMPREHENSIVE INCOME

For the six months ended June 30, 1999 and 1998 total comprehensive loss was as
follows (in thousands):




                                                                  June 30, 1999    June 30, 1998
                                                                  -------------    -------------
                                                                              
Net loss                                                              $(28,395)     $(18,216)

Other comprehensive income (loss):
Unrealized holding gains (losses) on investments                        (1,480)           89
Foreign currency translation adjustment                                   (107)         --
                                                                      --------      --------
Total other comprehensive income (loss)                                 (1,587)           89
                                                                      --------      --------

Total comprehensive loss                                              $(29,982)     $(18,127)
                                                                      --------      --------
                                                                      --------      --------



4.       RESTRUCTURED INVESTMENT IN ALTUS BIOLOGICS INC.

         Altus Biologics Inc. ("Altus") develops, manufactures and markets
products based on a novel and proprietary technology for stabilizing proteins.
At December 31, 1998, Vertex owned approximately 70% of the capital stock of
Altus. On February 5, 1999, Vertex restructured its investment in Altus. As part
of the transaction, Vertex provided Altus $3,000,000 of cash in exchange for
preferred stock and warrants. The preferred stock provides Vertex with a
minority ownership position in Altus, and the warrants become exercisable upon
certain events. As a result of the transaction, Altus now operates independently
from Vertex. In addition, Vertex has retained a non-exclusive royalty-free right
to use Altus' technology for discovering, developing and manufacturing small
molecule drugs. Vertex is recording its percentage of Altus' net income and
losses using the equity method of accounting.


5.       AGENERASE APPROVAL

         Agenerase(TM) was granted accelerated approval by the U.S. Food and
Drug Administration on April 15, 1999 for use in combination with other
antiretrovirals for the treatment of HIV infection. In connection with approval
of Agenerase, the Company earned a $5 million milestone payment under the
agreement with Glaxo Wellcome plc. Agenerase royalty revenue was recognized for
the first time in the second quarter of 1999.


6.       SUBSEQUENT EVENT

         In July 1999 the Company earned a $1,000,000 milestone payment from
Kissei Pharmaceutical Co., Ltd. ("Kissei") as a result of Kissei's filing for
approval to market ProzeiTM (amprenavir) in Japan. If and when approval is
granted, the Company will receive a royalty from sales of the drug.


                                      -9-






                MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                       CONDITION AND RESULTS OF OPERATIONS

THIS DISCUSSION CONTAINS FORWARD-LOOKING STATEMENTS WHICH ARE SUBJECT TO CERTAIN
RISKS AND UNCERTAINTIES THAT CAN CAUSE ACTUAL RESULTS TO DIFFER MATERIALLY FROM
THOSE DESCRIBED. FACTORS THAT MAY CAUSE SUCH DIFFERENCES INCLUDE BUT ARE NOT
LIMITED TO THOSE DESCRIBED IN THE SECTION OF THE COMPANY'S ANNUAL REPORT ON FORM
10-K ENTITLED "RISK FACTORS." READERS ARE CAUTIONED NOT TO PLACE UNDUE RELIANCE
ON THESE FORWARD-LOOKING STATEMENTS WHICH SPEAK ONLY AS OF THE DATE HEREOF. THE
COMPANY UNDERTAKES NO OBLIGATION TO PUBLICLY UPDATE OR REVISE THESE
FORWARD-LOOKING STATEMENTS TO REFLECT EVENTS OR CIRCUMSTANCES AFTER THE DATE
HEREOF.


         The Company is engaged in the discovery, development and
commercialization of novel, small molecule pharmaceuticals for the treatment of
major diseases for which there are currently limited or no effective treatments.
The Company is a leader in the use of structure-based drug design, an approach
to drug discovery that integrates advanced biology, biophysics, chemistry and
information technologies. The Company is conducting research and development
programs to develop pharmaceuticals for the treatment of viral diseases,
multidrug resistance in cancer, autoimmune and inflammatory diseases and
neurodegenerative disorders.

         The Company's lead product, AgeneraseTM (amprenavir), received U.S. FDA
approval through an expedited review process for the treatment of HIV infection
on April 15, 1999. Glaxo Wellcome plc ("Glaxo Wellcome"), Vertex's partner, has
also submitted applications for market approval to regulatory agencies in
countries throughout the world. The Company recognized royalties on sales of
Agenerase by Glaxo Wellcome for the first time this quarter. The Company has
incurred operating losses since its inception and expects to incur a loss in
1999. The Company believes that operating losses may continue beyond 1999 even
if significant royalties are realized on Agenerase sales because the Company is
planning to make significant investments in research and development for its
other potential products. The Company expects that losses will fluctuate from
quarter to quarter and that such fluctuations may be substantial.



RESULTS OF OPERATIONS

THREE MONTHS ENDED JUNE 30, 1999 COMPARED WITH THREE MONTHS ENDED JUNE 30, 1998.

         The Company's total revenues increased to $15,328,000 in the second
quarter of 1999 from $7,152,000 in the second quarter of 1998. In the second
quarter of 1999, revenues consisted of $2,874,000 in royalties and product
sales, $9,642,000 under the Company's collaborative agreements and other
revenue, and $2,812,000 in investment income. In the second quarter of 1998, the
Company received $3,247,000 in revenue from its collaborative agreements and
other revenue, and $3,905,000 in investment income.

         Royalties and product sales consist of Agenerase royalty revenue
from Glaxo Wellcome as well as initial sales of commercial drug substance to
Kissei in Japan. Agenerase royalty revenue from Glaxo Wellcome was recognized
for the first time in the quarter ended June 30, 1999 and is based upon the
world-wide sales of the drug net of actual and estimated discounts, rebates,
chargebacks, and product returns. This first quarter's sales reflect
prescriptions as well as initial trade stocking which Vertex expects will
adjust to be consistent with underlying demand over the remainder of the year.

         Payments under the Company's current collaborative agreements increased
from the second quarter of 1998 to the second quarter of 1999 primarily due to a
$5,000,000 milestone payment by Glaxo Wellcome for U.S. FDA approval of
Agenerase, a $1,000,000 payment by Schering AG for research support under a
collaborative agreement signed in August of 1998, and certain development


                                      -10-



reimbursements by collaborative partners for other programs. Investment income
decreased due to a lower level of cash and investments in the second quarter of
1999 as compared with the same period in 1998.

         The Company's total costs and expenses increased to $26,169,000 in
the second quarter of 1999 from $16,954,000 in the second quarter of 1998.
Royalties and product costs of $1,199,000, in the second quarter of 1999,
consist of royalty payments to G.D. Searle & Co. and the cost of commercial
drug substance sold to Kissei. Under the terms of the 1996 license agreement
between the Company, Glaxo Wellcome and G.D. Searle & Co. ("Searle"), the
Company agreed to pay Searle a royalty on the sales of Agenerase.

         Research and development expenses increased to $19,029,000 in the
second quarter of 1999 from $12,631,000 in the second quarter of 1998
principally due to the continued expansion of the Company's research
organization. Vertex's UK subsidiary expanded from a business development
operation to include scientific research and development staff and facilities
in the second half of 1998. The Company's development expenses increased due
to the continued growth in clinical trial activities, principally for the
manufacturing of clinical material and the initiation of clinical studies.

         General and administrative expenses increased to $5,466,000 in the
second quarter of 1999 from $4,164,000 in the second quarter of 1998. The
increase in general and administrative expenses principally reflects the
impact of personnel additions and an increase in marketing activities
associated with the launch of Agenerase. In addition, legal and patent
expenses have increased as the company continues to protect its intellectual
property and contests a suit filed by Chiron Corporation claiming
infringement of various U.S. patents issued to Chiron. While the final
outcome of the litigation with Chiron cannot be determined, the Company
believes, based on information currently available, that the ultimate outcome
of the action will not have a material impact on its consolidated financial
position.

         Using the equity method of accounting, the Company recorded $303,000 as
its share of the loss in Altus for the second quarter of 1999.

         Interest expense was $172,000 in the second quarter of 1999 as compared
to $159,000 in the second quarter of 1998 due to a higher blended interest rate
on similar levels of equipment lease financing during the year.

         For the reasons stated above, the Company recorded a net loss of
$10,841,000 or $0.43 per share in the second quarter of 1999 compared to a net
loss of $9,802,000 or $0.39 per share in the second quarter of 1998.


SIX MONTHS ENDED JUNE 30, 1999 COMPARED WITH SIX MONTHS ENDED JUNE 30, 1998.

         The Company's total revenues increased to $22,457,000 for the six
months ended June 30, 1999 from $14,321,000 for the six months ended June 30,
1998. In 1999, the Company's revenues consisted of $2,874,000 in royalties and
product sales, $13,605,000 under the Company's collaborative agreements and
other revenue, and $5,978,000 in investment income. In 1998, the Company's
revenues consisted of $6,420,000 earned under the Company's collaborative
agreements and $7,901,000 in investment income.

         Royalties and product sales consist of Agenerase royalty revenue from
Glaxo Wellcome as well as initial sales of commercial drug substance to Kissei
in Japan. Agenerase royalty revenue from Glaxo Wellcome was recognized for the
first time in the second quarter of 1999 and is based upon the world-wide sales
of the drug net of actual and estimated discounts, rebates, chargebacks, and
product returns. These sales reflect prescriptions as well as initial trade
stocking which Vertex expects will adjust to be consistent with underlying
demand over the remainder of the year.

         Revenue under the Company's collaborative agreements increased
$7,185,000 for the six months ended June 30, 1999 as compared with the same
period in 1998 primarily due to a $5,000,000 milestone payment by Glaxo
Wellcome for U.S. FDA approval of Agenerase and a $2,000,000 payment by
Schering

                                      -11-



AG for research support under a collaborative agreement signed in August of
1998. The decrease in investment income is due to lower cash and investment
levels for the first half of 1999 as compared with the first half of 1998.

         The Company's total costs increased to $50,852,000 for the six months
ended June 30, 1999 from $32,537,000 for the six months ended June 30, 1998.
Royalties and product costs of $1,199,000 consist of royalty payments to Searle
and the cost of commercial drug substance sold to Kissei in the second quarter
of 1999.

         Research and development expenses increased to $37,634,000 in the first
half of 1999 from $24,813,000 in the first half of 1998. The first half of 1999
includes expenses for the UK research and development staffing and facilities
growth initiated in the second half of 1998. Additionally, development expenses
were higher in the first half of 1999 due to the commencement of clinical trials
in the second half of 1998 and an increase in activities associated with the
Company's IMPDH program for psoriasis and hepatitis C, its neurophilins program
for diabetic neuropathy, and its P38 program for inflammatory diseases.

         General and administrative expenses increased during the first half of
1999 to $11,238,000 from $7,417,000 in the first half of 1998 due primarily to
increases in personnel and professional expenses, particularly associated with
the market launch of Agenerase and corporate advertising activities. Legal and
patent expenses have increased as the Company continues to protect its
intellectual property and contests a suit filed by Chiron Corporation.

         Using the equity method of accounting, the Company recorded $425,000 as
its share of the loss in Altus in the first half of 1999.

          Interest expense was $356,000 in the first half of 1999, an increase
from $307,000 in the first half of 1998 due to a higher blended interest rate on
similar levels of equipment lease financing during the year.

         For the reasons stated above, the Company incurred a net loss of
$28,395,000 or $1.12 per share in the six months ended June 30, 1999 compared to
a net loss of $18,216,000 or $0.72 per share in the six months ended June 30,
1998.

LIQUIDITY AND CAPITAL RESOURCES

         The Company's operations have been funded principally through
strategic collaborative agreements, public offerings and private placements
of the Company's equity securities, equipment lease financing, and investment
income. The Company expects to incur increased research and development and
related supporting expenses and, consequently, may continue to experience
losses on a quarterly and annual basis as it continues to develop existing
and future compounds and conduct clinical trials of potential drugs. The
Company also expects to incur substantial administrative and
commercialization expenditures in the future and additional expenses related
to the filing, prosecution, defense and enforcement of patent and other
intellectual property rights.

         The Company expects to finance these substantial cash needs with
royalties from the sale of Agenerase, its existing cash and investments of
approximately $205 million at June 30, 1999, together with investment income
earned thereon, future payments under its existing and future collaborative
agreements, and facilities and equipment financing. To the extent that funds
from these sources are not sufficient to fund the Company's activities, it will
be necessary to raise additional funds through public offerings or private
placements of securities or other methods of financing. There can be no
assurance that such financing will be available on acceptable terms, if at all.


                                      -12-



The Company's aggregate cash and investments decreased by $40,660,000 during
the six months ended June 30, 1999 to $204,992,000. Cash used by operations
was $27,491,000 during the same period. Prepaids and other current assets
have increased $3,286,000 during the first half of 1999 due primarily to the
recording of a royalty receivable from Glaxo Wellcome for Agenerase sales.
Restricted cash increased $1,882,000 during the six months ended June 30,
1999 as the Company issued a letter of credit for a security deposit under
one of the Company's facilities leases. This was for the takedown of
additional, available space at the end of 1998. The Company continues to
invest in equipment and leasehold improvements for its facilities to match
the growth in its headcount. The Company also restructured its investment in
Altus and as part of the transaction Vertex provided Altus $3,000,000 of cash
in exchange for new classes of preferred stock and warrants. As a result of
the transaction, Altus now operates independently from Vertex.

YEAR 2000

         The Company is conducting a program to address the impact of the Year
2000 on the processing of date sensitive information by the Company's computer
systems and software ("IT Systems"), embedded systems in its non-computer
equipment ("Non-IT Systems") and relationships with certain third parties.

         In the first stage of the program, the Company determined which IT
Systems, Non-IT Systems and third party relationships were critical to the
Company's business. This review has been completed. The Company does not intend
to perform a comprehensive review of systems and third parties that are not
deemed critical, and the Company cannot guarantee that such systems and entities
will be Year 2000 compliant.

         The Company has completed its assessment of its critical IT Systems and
determined the actions necessary in order to ensure that they will function
without disruption. Based on this assessment, the Company has begun remediation
and testing of certain critical IT Systems. The Company expects that remediation
of all critical IT Systems will be completed by the end of August 1999 and
testing will be completed by the end of September 1999.

         The Company has completed its assessment and is currently in the
process of remediation and testing of its critical Non-IT Systems for Year 2000
compliance. The Company expects that remediation of non-compliant critical
Non-IT Systems will be completed by the end of August 1999 and testing will be
completed by the end of September 1999. Some critical Non-IT Systems are
non-compliant and, because of the age of those systems or other factors, cannot
be made compliant. The Company intends to formulate contingency plans for each
of those systems by the end of the third quarter of 1999.

         The Company has contacted third parties that provide goods, services
and information that are deemed critical to the Company's business. The Company
is currently reviewing the responses and Year 2000 website statements of these
entities to assess their Year 2000 compliance. The Company expects to formulate
contingency plans by the end of October 1999 for the services provided by third
parties that are found to be non-compliant, or where the Company is unable to
determine whether a third party is compliant. There can be no assurance,
however, that the Company will be able to locate alternate sources for goods or
services furnished by non-compliant providers.

         The Company is using both internal and external resources to conduct
its Year 2000 program. The Company believes that the total costs, both out-of
pocket and internal, of the Company's Year 2000 program will not be material.
The Company plans to fund these Year 2000 costs through available cash. However,
the Company may experience unexpected costs in achieving full Year 2000
compliance which could result in a material adverse effect on the Company's
results of operations. Other IT Systems projects have not been significantly
deferred as a result of the Company's Year 2000 program, because the Company was
able to integrate much of its Year 2000 assessment and remediation effort into
its routine maintenance and upgrade programs.

         There can be no assurance that the Company's Year 2000 assessment and
any required remedial actions and contingency plans will be successfully
completed on a timely basis.


                                      -13-



QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

         There are no material changes to the Company's assessment of market
risk as disclosed in its 10-K filing for the year ended December 31, 1998.



                                    PART II.

                                OTHER INFORMATION



Item 1.  LEGAL PROCEEDINGS:

                  None

Item 2.  CHANGES IN SECURITIES:

                  None

Item 3.  DEFAULTS UPON SENIOR SECURITIES:

                  None

Item 4.  SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS:

         The Company's Annual Meeting of Stockholders was held on May 19, 1999.
The stockholders elected Roger W. Brimblecombe and Donald R. Conklin to the
class of directors whose term expires in 2002. The tabulation of votes with
respect to the election of such directors is as follows:




                                  Total Vote For:   Total Vote Withheld:
                                  ---------------   --------------------
                                                    
Roger W. Brimblecombe               18,513,349            107,522
Donald R. Conklin                   18,513,949            106,922


         The stockholders approved an amendment to the Company's 1996 Stock and
Option Plan, authorizing the addition of 1,250,000 shares to that plan, with
7,838,590 shares voted in favor, 6,076,014 shares voted against, 21,025 shares
abstaining, and 4,685,242 broker non-votes.

         The stockholders also approved an amendment to the Company's Employee
Stock Purchase Plan, authorizing the addition of 200,000 shares to that plan,
with 11,863,447 shares voted in favor, 2,061,792 shares voted against, 10,390
shares abstaining, and 4,685,242 broker non-votes.

         In addition, the stockholders approved the appointment of
PricewaterhouseCoopers LLP as the Company's independent accountants for the 1999
fiscal year by a vote of 18,594,651 shares in favor, 19,405 shares against, and
6,815 shares abstaining.


Item 5.  OTHER INFORMATION:
                  None


                                      -14-



Item 6.  EXHIBITS:

                  27   Financial Data Schedule. (Exhibit 27 is submitted as an
                       exhibit only in the electronic format of this Quarterly
                       Report on Form 10-Q submitted to the Securities and
                       Exchange Commission.)

                  99   Letter of Independent Accountants

         REPORTS ON FORM 8-K:
                      None


                                   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.

                                       VERTEX PHARMACEUTICALS INCORPORATED




Date:  August 14, 1999                 /s/ Thomas G. Auchincloss
                                       ---------------------------------------
                                       Thomas G. Auchincloss, Jr.
                                       Vice President of Finance and Treasurer
                                       (Principal Financial Officer)



Date:  August 14, 1999                 /s/ Hans D. van Houte
                                       ---------------------------------------
                                       Hans D. van Houte
                                       Controller and Assistant Treasurer
                                       (Principal Accounting Officer)


                                      -15-