<PAGE>


                       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 October 31, 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: 0-27756


                          Alexion Pharmaceuticals, Inc.
                        ---------------------------------
             (Exact name of registrant as specified in its charter)

            Delaware                                      13-3648318
         ---------------                             ------------------
         (State or other                             (I.R.S. Employer
         jurisdiction of                             Identification No.)
         incorporation or
         organization)

            25 Science Park, Suite 360, New Haven, Connecticut 06511
           ----------------------------------------------------------
               (Address of principal executive offices) (Zip Code)

                                  203-776-1790
                                ----------------
              (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
            --------          ---------


            Class                              Outstanding at December 9, 1998
- -------------------------------                -------------------------------
Common Stock, $0.0001 par value                          11,281,324



<PAGE>


                          ALEXION PHARMACEUTICALS, INC.

                                      INDEX




<TABLE>
<CAPTION>

                                                                                 Page
                                                                                 ----

PART I.           FINANCIAL INFORMATION

<S>                                                                              <C>

         Item 1.  Financial Statements

                  Balance Sheets as of October 31, 1998
                  and July 31, 1998                                               3

                  Statements of Operations for the three months ended
                  October 31, 1998 and 1997                                       4

                  Statements of Cash Flows for the three months ended
                  October 31, 1998 and 1997                                       5

                  Notes to Financial Statements                                   6



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




PART II.          OTHER INFORMATION                                              14



SIGNATURES                                                                       15

</TABLE>




                                  Page 2 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.

                                 Balance Sheets
                (dollars in thousands, except per share amounts)



<TABLE>
<CAPTION>

                                                                 October 31, 1998    July 31, 1998
                                                                 ----------------    -------------
                            ASSETS                                (UNAUDITED)
<S>                                                                     <C>                <C>    
Current Assets:
     Cash and cash equivalents                                          $29,607            $31,509
     Marketable securities                                                4,045              5,985
     Prepaid expenses                                                       169                209
     Other current assets                                                   -                  137
                                                                        -------            -------
               Total current assets                                      33,821             37,840
                                                                        -------            -------
Equipment, net of accumulated
     depreciation and amortization                                        2,411              2,357
                                                                        -------            -------
Other Assets:
     License technology rights, net                                         132                154
     Patent application costs, net                                          144                149
     Security deposits and other assets                                   1,589              1,585
                                                                        -------            -------
               Total other assets                                         1,865              1,888
                                                                        -------            -------

                         TOTAL ASSETS                                   $38,097            $42,085
                                                                        -------            -------
                                                                        -------            -------
             LIABILITIES AND STOCKHOLDERS' EQUITY
Current Liabilities:
     Current portion of notes payable                                      $368               $368
     Accounts payable                                                       763                810
     Accrued expenses                                                       613                818
     Deferred revenue                                                        67                 67
                                                                        -------            -------
               Total current liabilities                                  1,811              2,063
                                                                        -------            -------

Notes Payable, less current portion included above                          740                832

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

Stockholders' Equity:
     Common stock $.0001 par value;  25,000,000 shares
          authorized; 11,236,987 and 11,236,987 shares issued
          at October 31, 1998 and July 31, 1998, respectively                 1                  1
     Additional paid-in capital                                          79,797             79,781
     Deficit accumulated                                                (44,252)           (40,592)
     Treasury stock, at cost;  11,875 shares                               -                   -
                                                                        -------            -------
               Total stockholders' equity                                35,546             39,190

                                                                        -------            -------
               TOTAL LIABILITIES AND NET EQUITY                         $38,097            $42,085
                                                                        -------            -------
                                                                        -------            -------

</TABLE>


                         See accompanying notes to financial statements.


                                  Page 3 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.

                            Statements of Operations
                                   (UNAUDITED)
                (dollars in thousands, except per share amounts)

<TABLE>
<CAPTION>

                                                                 Three months ended October 31,
                                                                 ------------------------------
                                                                      1998            1997
                                                                 -------------- ---------------
<S>                                                             <C>             <C>         
CONTRACT RESEARCH REVENUES                                      $        255    $      4,126
                                                                ------------    ------------
OPERATING EXPENSES:
    Research and Development                                           3,784           2,360
    General and Administrative                                           628             587
                                                                ------------    ------------
    Total Operating Expenses                                           4,412           2,947
                                                                ------------    ------------
OPERATING INCOME(LOSS)                                                (4,157)          1,179

OTHER INCOME, Net                                                        497             444
                                                                ------------    ------------

NET INCOME(LOSS)                                                      (3,660)          1,623

ACCRETION OF PREFERRED STOCK DIVIDENDS                                     0             300
                                                                ------------    ------------
NET INCOME(LOSS) APPLICABLE TO
COMMON SHAREHOLDERS                                             ($     3,660)   $      1,323
                                                                ------------    ------------
                                                                ------------    ------------
BASIC NET INCOME(LOSS) PER COMMON SHARE
 (Note 3)                                                       ($      0.33)   $       0.15
                                                                ------------    ------------
                                                                ------------    ------------
SHARES USED IN COMPUTING BASIC NET
   INCOME(LOSS) PER COMMON SHARE                                  11,225,851       8,952,434
                                                                ------------    ------------
                                                                ------------    ------------
DILUTED NET INCOME(LOSS) PER COMMON SHARE
 (Note 3)                                                       ($      0.33)   $       0.13
                                                                ------------    ------------
                                                                ------------    ------------
SHARES USED IN COMPUTING DILUTED NET
   INCOME(LOSS) PER COMMON SHARE                                  11,225,851       9,861,222
                                                                ------------    ------------
                                                                ------------    ------------
</TABLE>


              See accompanying notes to financial statements.


                                  Page 4 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.

                            Statements of Cash Flows
                                   (UNAUDITED)
                             (dollars in thousands)


<TABLE>
<CAPTION>

                                                                    Three months ended October 31,
                                                                    ---------------------------

                                                                        1998          1997
                                                                    -------------  ------------
<S>                                                                      <C>            <C>   
CASH FLOWS FROM OPERATING ACTIVITIES:
    Net income(loss)                                                     ($3,660)       $1,623
    Adjustments to reconcile net income(loss) to net cash
            used in operating activities:
       Depreciation and amortization                                         163           139
       Change in assets and liabilities:
          Prepaid expenses                                                    40            11
         Other current assets                                                137             0
         Accounts payable                                                    (47)          283
         Accrued expenses                                                   (205)         (293)
         Deferred revenue                                                      0          (280)
                                                                    -------------  ------------
            Net cash (used in) provided by operating activities           (3,572)        1,483

CASH FLOWS FROM INVESTING ACTIVITIES:
    Proceeds from marketable securities, net                               1,956             1
    Purchases of equipment                                                  (188)         (163)
    Patent application costs                                                  (2)            1
                                                                    -------------  ------------
            Net cash provided by (used in) investing activities            1,766          (161)

CASH FLOWS FROM FINANCING ACTIVITIES:
    Net proceeds from issuance of preferred and common stock                   0        13,488
    Repayments of capital lease obligations                                    0            (5)
    Repayments of notes payable                                              (92)          (77)
    Security deposits and other assets                                        (4)            0
                                                                    -------------  ------------
            Net cash (used in) provided by financing activities              (96)       13,406

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

NET (DECREASE) INCREASE  IN CASH                                          (1,902)       14,728


CASH and CASH EQUIVALENTS at beginning of period                          31,509        16,742

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

CASH AND CASH EQUIVALENTS at end of period                               $29,607       $31,470

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


SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION
    Cash paid for interest expense                                           $23            $4
                                                                    -------------  ------------
                                                                    -------------  ------------

SUPPLEMENTAL DISCLOSURE OF NONCASH FINANCING ACTIVITIES
    Preferred stock dividend accretion                                        $0          $300
                                                                    -------------  ------------
                                                                    -------------  ------------

</TABLE>


                       See accompanying notes to financial statements.



                                  Page 5 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                   (Unaudited)


1.   Operations and Basis of Presentation -

Alexion Pharmaceuticals, Inc. ("Alexion" or the "Company") was organized in 1992
and is a biopharmaceutical company engaged in the research and development of
proprietary immunoregulatory compounds for the treatment of acute coronary
syndromes (cardiopulmonary bypass, acute myocardial infarction, coronary
angioplastry, and unstable angina) and autoimmune diseases (systemic lupus,
rheumatoid arthritis, multiple sclerosis and diabetes mellitus). The Company is
currently conducting clinical trials in CPB, rheumatoid arthritis, and systemic
lupus patients. As an outgrowth of its core technologies, the Company has been
developing, in collaboration with third parties (see Note 5), non-human
("xenograft") cell and organ products designed for transplantation into humans
without clinical rejection. Additional development programs include product
candidates to treat spinal cord injury, Parkinson's disease and solid organ
failure.

The Company has incurred losses since inception and has cumulative net losses of
approximately $44.2 million through October 31, 1998. The Company has made no
product sales to date and has recognized cumulative revenue from research grants
and funding of $12.0 million through October 31, 1998.

The Company will need additional financing to obtain regulatory approvals, fund
operating losses, and, if deemed appropriate, establish a manufacturing, sales,
and marketing capability. In addition the Company operates in an environment of
rapid change in technology and substantial competition from pharmaceutical and
biotechnology companies and is dependent upon the services of its employees and
its consultants.

The Company expects to incur substantial expenditures in the foreseeable future
for the research and development and commercialization of its products. The
Company's management believes that, based upon its current business plans, the
cash and marketable securities aggregating $33.7 million as of October 31, 1998
will be sufficient to fund operations of the Company through the next eighteen
months.

The Company will require funds in addition to those previously described, which
it will seek to raise through public or private equity or debt financings,
collaborative or other arrangements with corporate sources, or through other
sources of financing. During 1998, the Company obtained a term loan facility for
$1.2 million with a commercial bank for the financing of capital expenditures
principally related to facilities manufacturing scale-up equipment (see Note 7).
The Company has no other capital sources and no arrangements or commitments with
regard to obtaining any further funds.


                                  Page 6 of 16

<PAGE>

                          ALEXION PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                   (Unaudited)


Prior to July 31, 1998, the Company reported as a development stage entity.

The financial statements included herein have been prepared by the Company,
without audit, pursuant to the rules and regulations of the Securities and
Exchange Commission ("SEC") and include, in the opinion of management, all
adjustments, consisting of normal, recurring adjustments, necessary for a fair
presentation of interim period results. Certain information and footnote
disclosures normally included in financial statements prepared in accordance
with generally accepted accounting principles have been condensed or omitted
pursuant to such rules and regulations. The results for the interim periods
presented are not necessarily indicative of results to be expected for any
future period. It is suggested that these condensed financial statements be read
in conjunction with the audited financial statements and notes thereto included
in the Company's Form 10-K Annual Report for the fiscal year ended July 31,
1998.


2.   Cash and Cash Equivalents and Marketable Securities -

Cash and cash equivalents are stated at cost, which approximates market, and
include short-term highly liquid investments with original maturities of less
than three months.

The Company invests in marketable securities of highly rated financial
institutions and investment-grade debt instruments and limits the amount of
credit exposure with any one entity. The Company has classified its marketable
securities as "available for sale" and, accordingly, carries such securities at
aggregate fair value. Unrealized gains or losses are included in stockholders'
equity as a component of additional paid-in capital.


3.   Net Income (Loss) Per Share -

In February 1997, the Financial Accounting Standards Board issued SFAS No. 128,
"Earnings Per Share", which superceded Accounting Principles Board Opinion 15.
This new standard replaces the computation of "basic earnings (loss) per share".
The Company adopted this standard for all periods ending on or after January 31,
1998. Previously reported net income (loss) per common share is required to be
restated under the provisions of SFAS No. 128. Accordingly, reported net income
per share for the three months ended October 31, 1997 has been restated to
conform with this new standard.


                                  Page 7 of 16

<PAGE>

                          ALEXION PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                   (Unaudited)


4.   Revenue Recognition -

Contract research revenues are recognized as the related work is performed under
the terms of the contracts and expenses for development activities are incurred.
Any revenue contingent upon future funding by the Company is deferred and
recognized as the future funding is expended. Any revenues resulting from the
achievement of milestones would be recognized when the milestone is achieved.
License fee revenues represent non-refundable payments received in accordance to
contractual agreements for various access and rights to the Company's
technologies, research, potential products and markets.


5.   Revenues -

Revenues recorded by the Company consist of license fees and research and
development support under collaborations with United States Surgical Corporation
("US Surgical") and Genetic Therapy, Inc. ("GTI/Novartis"), and funding from the
Commerce Department's National Institute of Standards and Technology ("NIST")
through the grants from Advanced Technology Program ("ATP").

In July 1995, the Company entered into a collaborative research and development
agreement with US Surgical. US Surgical agreed to fund pre-clinical development
of the Company's xenotransplant products in return for exclusive worldwide
manufacturing, marketing and distribution rights of such products by paying the
Company up to $7.5 million allocated as follows: (1) up to $4.0 million of the
cost of pre-clinical development, all of which have been paid as of October 31,
1997 and (2) $3.5 million upon achieving certain milestones. In furtherance of
this joint collaboration, US Surgical also purchased $4.0 million of the
Company's common stock. At the end of September 1997, US Surgical and the
Company modified the research and development agreement. As part of the
modification, US Surgical made an additional $6.5 million payment to the Company
for equity, exclusive licensing rights, and certain manufacturing assets.
Further, as part of the modified agreement, US Surgical and the Company agreed
that the pre-clinical milestone payment in the original agreement was considered
to have been satisfied. On October 1, 1998, US Surgical completed a merger with
a subsidiary of Tyco International Ltd. The Company believes that although the
relationship with US Surgical may be modified as a result of the merger, the
Company will be able to continue to develop xenotransplantation products.
However, there can be no assurance that any such modification would not have an
adverse effect on the Company or such products.

In December 1996, Alexion and GTI/Novartis entered into a License and
Collaborative Research Agreement with respect to the Company's gene transfer
technology. GTI/Novartis agreed to fund 


                                  Page 8 of 16

<PAGE>
                          ALEXION PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                   (Unaudited)


a minimum of $400,000 per year for two years for research and development
support by Alexion. In October 1998, in view of Alexion's increased focus on the
advanced clinical development of its anti-inflammatory drug candidates and
GTI/Novartis's recently announced restructuring and reorganization, the Company
and GTI/Novartis agreed to discontinue the collaborative gene therapy program.


6.   Equity Offerings -

In September 1997, the Company completed the private placement of 400,000 shares
of Series B Preferred Stock for aggregate consideration of $10,000,000 to a
single institutional investor, Biotech Target S.A. The net proceeds to the
Company were approximately $9.5 million. The investor was entitled to a dividend
of $2.25 per share of Series B Preferred Stock if this stock was held through
March 4, 1998. In March 1998 the investor converted the preferred stock into
935,782 shares of common stock and dividends of $900,000 were paid by the
delivery of an additional 70,831 shares of the Company's common stock. In March
1998, Biotech Target S.A. purchased an additional 670,000 shares of common stock
for aggregate consideration of approximately $8,800,000.

 In September 1997, the Company sold 166,945 shares of its common stock to US
Surgical for aggregate consideration of $3,000,000 The sale of common stock was
made in connection with the modification of the joint development agreement
between the Company and US Surgical.

In connection with its private placements in fiscal 1993 and 1994, the Company
had issued warrants to purchase common stock. These warrants were exercisable at
any time prior to the close of business on December 4, 1997. During the quarter
ended October 31, 1997, warrants were exercised for the purchase of 124,213
shares of common stock aggregating approximately $938,000 of proceeds to the
Company.


7.   Notes Payable -

As of July 31, 1998, a term loan was used to finance the purchase of capital
equipment The term loan requires quarterly principal payments of $92,000
commencing August 3, 1998 and payable through August 2001. The notes payable
balance was $1.1 million at October 31, 1998. The term loan agreement requires
the Company to maintain a restricted cash balance of $1.5 million, in an
interest bearing account as collateral for the note. The restricted cash balance
is subject to reductions on an annual basis.


                                  Page 9 of 16

<PAGE>
                          ALEXION PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                   (Unaudited)



8.   Preferred Stock Dividend Accretion -

In September 1997, the Company began accruing a dividend payable to Biotech
Target S.A. of $2.25 per share of Series B Preferred Stock related to this
private placement. The dividend was payable in either cash or common stock. The
Company had recognized $300,000 of dividends payable through October 31, 1997.
In March 1998, the Company paid all dividends owed to this investor (see Note
6).

9.   Comprehensive Income(Loss) -

Effective August 1, 1998, the Company adopted SFAS No. 130 "Reporting
Comprehensive Income". This statement establishes standards for reporting and
display of comprehensive income(loss) and its components within financial
statements. There was no significant difference between net income(loss) and
comprehensive income(loss) for the three month periods ended October 31, 1998
and 1997.


                                 Page 10 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.



I
tem 2. Management's Discussion and Analysis of Financial Condition and Results
        of Operations


This report contains forward-looking statements which involve risks and
uncertainties. Such statements are subject to certain factors and uncertainties
which may cause the Company's plans and results to differ significantly from
plans and results discussed in such forward-looking statements. Factors that
might cause or contribute to such differences include, but are not limited to,
the rate of progress, if any, of the Company's research and development
programs, the Company's ability to compete successfully, the Company's ability
to attract and retain qualified personnel, the Company's ability to successfully
enter into collaborations with third parties, the Company's ability to enter
into and progress in clinical trials, the time and costs involved in obtaining
regulatory approvals, the costs involved in obtaining and enforcing patents and
any necessary licenses, the ability of the Company to establish development and
commercialization relationships and strategic alliances with third parties, the
cost of manufacturing, the Company's ability to obtain additional funds, and
those other risks discussed in Exhibit 99 to the Company's Annual Report on Form
10-K for the fiscal year ended July 31, 1998.


Overview

Since its inception in January 1992, Alexion has devoted substantially all of
its resources to its drug discovery, research and product development programs.
To date, the Company has not received any revenues from the sale of products.
The Company has been unprofitable since inception, and expects to incur
substantial and increasing operating losses for the next several years due to
expenses associated with product research and development, pre-clinical and
clinical testing, regulatory activities and manufacturing development and
scale-up. As of October 31, 1998, the Company has an accumulated deficit of
$44.2 million.

The Company's plan is to develop and commercialize on its own those product
candidates for which the clinical trial and marketing requirements can be funded
by the Company. For certain of the Company's C5 Inhibitor and Apogen products
for which greater resources will be required, Alexion's strategy is to form
corporate partnerships with major pharmaceutical companies for product
development and commercialization.

The Company recognizes research and development revenues when the development
expenses are incurred and the related work is performed under the terms of the
contracts. Any revenue contingent upon future expenditures by the Company is
deferred and recognized as the future expenditures are incurred. Any revenues
contingent upon the achievement of milestones will be recognized when the
milestones are achieved.


                                 Page 11 of 16

<PAGE>
                          ALEXION PHARMACEUTICALS, INC.



Results of Operations

         Three Months Ended October 31, 1998
         Compared with Three Months Ended October 31, 1997

The Company's contract research and license revenues decreased to $255,000 for
the three months ended October 31, 1998 from $4,126,000 for the same period
ended October 31, 1997. This decrease was due primarily to a one-time license
fee of $3,500,000 the Company received from US Surgical in connection with the
September 1997 modification of the companies' collaborative research and
development agreement.

Research and development expenses increased to $3,784,000 for the three months
ended October 31, 1998 from $2,360,000 for the three months ended October 31,
1997. The increase resulted principally from incurred costs related to clinical
trials of the Company's lead C5 Inhibitors, 5G1.1-SC and 5G1.1, and contract
manufacturing costs for the Company's recombinant product candidates.

General and administrative related expenses increased to $628,000 for the three
months ended October 31, 1998 from $587,000 for the same period ended October
31, 1997. The increase in general and administrative expenses resulted
principally from higher expenses in office equipment and services, and
telecommunication fees related to increased personnel.

The Company earned other income, net, of $497,000 for the three months ended
October 31, 1998 as compared to other income, net, of $444,000 for the same
three month period ended October 31, 1997. This other income, net, resulted
principally from greater interest income on higher cash balances available for
investment.

As a result of the above factors, the Company incurred net loss of $3,660,000
for the three months ended October 31, 1998 as compared to net income of
$1,623,000 for the same three month period in 1997.


                                 Page 12 of 16

<PAGE>


                          ALEXION PHARMACEUTICALS, INC.


Liquidity and Capital Resources

As of October 31, 1998, the Company had working capital of $32.0 million,
including $33.7 million of cash, cash equivalents and marketable securities.
This compares with working capital at October 31, 1997, of $35.4 million,
including $37.5 million of cash, cash equivalents and marketable securities. The
decrease in working capital was due to the costs of operating the business.

The Company leases its administrative and research and development facilities
under three operating leases expiring in December 1997, June 1998, and March
1999. The Company is currently continuing the lease that expired in December
1997 and June 1998 on a month-to-month basis while discussions for lease
extensions are on going.

The Company anticipates that its existing available capital resources and
interest earned on available cash and marketable securities should be sufficient
to fund its operating expenses and capital requirements as currently planned
through the next eighteen months. While the Company currently has no material
commitments for capital expenditures, the Company's future capital requirements
will depend on many factors, including the progress of the Company's research
and development programs, progress in clinical trials, the time and costs
involved in obtaining regulatory approvals, the costs involved in obtaining and
enforcing patents and any necessary licenses, the ability of the Company to
establish development and commercialization relationships, and the costs of
manufacturing scale-up.

The Company expects to incur substantial additional costs, including costs
associated with research, pre-clinical and clinical testing, manufacturing
process development, and additional capital expenditures associated with
facility expansion and manufacturing requirements in order to commercialize its
products currently under development. The Company will need to raise substantial
additional funds through additional financings including public or private
equity offerings and collaborative research and development arrangements with
corporate partners. There can be no assurance that funds will be available on
terms acceptable to the Company, if at all, or that discussions with potential
collaborative partners will result in any agreements on a timely basis, if at
all. The unavailability of additional financing could require the Company to
delay, scale back or eliminate certain of its research and product development
programs or to license third parties to commercialize products or technologies
that the Company would otherwise undertake itself, any of which could have a
material adverse effect on the Company.


                                 Page 13 of 16

<PAGE>

                          ALEXION PHARMACEUTICALS, INC.


YEAR 2000

The "Year 2000" (or "Y2K") issue affects computer and information technology
("IT") systems, as well as non-IT systems which include embedded technology such
as micro-processors and micro-controllers (or micro-chips) that have date
sensitive programs that may not properly recognize the year 2000. Systems that
do not properly recognize such information could generate inaccurate data or
cause a system to fail, resulting in business interruption. The Company is
currently developing a plan to provide measured assurances that its computer and
IT-systems, non-IT systems, including embedded systems such as HVAC (heating,
ventilation and air conditioning) systems and other analytical instruments and
equipment, and those of third parties which have a material relationship with
the Company are or will be Y2K compliant.

The Company has begun, but has not yet completed a comprehensive inventory and
assessment of its existing IT and non-IT systems, including planned systems.
This inventory and assessment is expected to be completed next quarter. The
Company will survey key third parties and third parties' services which the
Company may purchase or use, respectively, with regards to their IT systems and
Y2K compliance. Assessment will include identifying critical systems -- internal
and external (including third parties) -- in order to formulate a remediation
and verification plan. The Company currently believes that remediation and
verification, which include obtaining written assurances from key vendors and
suppliers, as well as testing, will be complete by July 1999.

The Company believes, based on preliminary information, that the costs
associated with remediation and verification to become Y2K compliant will not
have a material adverse impact on the Company's financial position, results of
operations, or cash flow. In the event that the Company's Y2K compliance plan is
not successfully implemented, the Company may experience temporary disruptions
of the Company's clinical trial sites as well as external contract manufacturing
of the Company's therapeutic products - presuming broad Y2K compliance by
general service providers such as utilities, telephone, data transfer, and other
government and private entities. While the Company has not yet developed
contingency plans for such event, the Company expects to prepare such plans by
August 1999.

Although the Company has taken steps to address the Y2K problem, there can be no
assurance that the failure of the Company and/or its material third parties to
timely attain Y2K compliance or that the failures and/or the impacts of broader
compliance failures by telephone, mail, data transfer or other utility or
general service providers or government or private entities will not have a
material adverse effect on the Company. Further, there can be no assurance that
the cost associated with achieving such compliance or any failure to become Y2K
compliant will not be material to the Company's financial position, its results
of operations, or cash flow.


                                 Page 14 of 16

<PAGE>


P
ART II.            OTHER INFORMATION




Item 5.             Other Information.  None



Item 6.             Exhibits and Reports on Form 8-K (a) Exhibits

                    Exhibit 11 - Calculation of earnings per share 
                    Exhibit 27 - Article 5 Financial Data Schedule for 
                    1st Quarter 10-Q


                    (b) Reports on Form 8-K
                  
                    During the quarter for which this report is filed, the
                    Company filed a current report on Form 8-K, dated October 8,
                    1998, regarding the Company's fourth quarter and year end
                    results for the fiscal year ended July 31, 1998.


                                 Page 15 of 16

<PAGE>






                                   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.

                                       ALEXION PHARMACEUTICALS, INC.



Date:  December 14, 1998               By:/s/ Leonard Bell, M.D.
                                           -------------------------------------
                                          Leonard Bell, M.D.
                                          President and Chief Executive Officer,
                                          Secretary and Treasurer (principal 
                                          executive officer)


Date:  December 14, 1998               By:/s/ David W. Keiser
                                           -------------------------------------
                                          David W. Keiser
                                          Executive Vice President and Chief 
                                          Operating Officer (principal financial
                                          officer)


Date:  December 14, 1998                By:/s/ Barry P. Luke
                                           -------------------------------------
                                            Barry P. Luke
                                            Vice President of Finance and 
                                            Administration(principal accounting 
                                            officer)


                                 Page 16 of 16





<PAGE>

                                                                      Exhibit 11

                          ALEXION PHARMACEUTICALS, INC.
                        EXHIBIT 11. - Earnings Per Share
                                   (UNAUDITED)


<TABLE>
<CAPTION>
                                                     Three months ended October 31,
                                                        1998                1997
                                                      -----------    -----------
<S>                                                    <C>             <C>      

  Average shares outstanding ......................    11,225,851      8,952,434
  Net effect of dilutive stock options
    and warrants based on the treasury
    stock method using average market price .......             0        908,788
                                                      -----------    -----------
         TOTALS ...................................    11,225,851      9,861,222
                                                      -----------    -----------


Net Income (loss) applicable to common stockholders    (3,659,733)     1,322,641
                                                      -----------    -----------

Diluted Net Income (loss) per share ..............    $    (0.33)   $      0.13
                                                      -----------    -----------
</TABLE>






<TABLE> <S> <C>


<PAGE>
<ARTICLE> 5
<LEGEND>
THIS SCHEDULE CONTAINS SUMMARY FINANCIAL INFORMATION EXTRACTED FROM THE BALANCE
SHEET, THE STATEMENT OF OPERATIONS, AND THE STATEMENT OF CASH FLOWS AND IS
QUALIFIED IN ITS ENTIRETY BY REFERENCE TO SUCH FINANCIAL STATEMENTS.  ALL
PREVIOUSLY REPORTED NET EARNINGS (LOSS) PER COMMON SHARE HAVE BEEN REFLECTED IN
SFAS NO. 128.
</LEGEND>
<MULTIPLIER> 1,000
       
<S>                             <C>
<PERIOD-TYPE>                   3-MOS
<FISCAL-YEAR-END>                          JUL-31-1999
<PERIOD-START>                             AUG-01-1998
<PERIOD-END>                               OCT-31-1998
<CASH>                                          29,607
<SECURITIES>                                     4,045
<RECEIVABLES>                                        0
<ALLOWANCES>                                         0
<INVENTORY>                                          0
<CURRENT-ASSETS>                                33,821
<PP&E>                                           5,545
<DEPRECIATION>                                 (3,134)
<TOTAL-ASSETS>                                  38,097
<CURRENT-LIABILITIES>                            1,811
<BONDS>                                            740
<PREFERRED-MANDATORY>                                0
<PREFERRED>                                          0
<COMMON>                                             1
<OTHER-SE>                                      35,545
<TOTAL-LIABILITY-AND-EQUITY>                    38,097
<SALES>                                              0
<TOTAL-REVENUES>                                   255
<CGS>                                                0
<TOTAL-COSTS>                                    4,412
<OTHER-EXPENSES>                                     0
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                               (497)
<INCOME-PRETAX>                                (3,660)
<INCOME-TAX>                                         0
<INCOME-CONTINUING>                            (3,660)
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                   (3,660)
<EPS-PRIMARY>                                   (0.33)
<EPS-DILUTED>                                   (0.33)
        

</TABLE>