<Page>

                                                                     EXHIBIT 4.1

                          ALEXION PHARMACEUTICALS, INC.
                             2000 STOCK OPTION PLAN

                  1. PURPOSE. The purpose of the Alexion Pharmaceuticals, Inc.
2000 Stock Option Plan (the "Plan") is to establish a vehicle through which
Alexion Pharmaceuticals, Inc. (the "Company") can make discretionary grants of
Options to purchase shares of the Company's common stock, par value $0.0001 (the
"Common Stock") to members of the Board of Directors of the Company (the
"Board"), to officers and other employees of the Company and its Affiliates and
to consultants and other independent contractors of the Company and its
Affiliates, with a view toward promoting the long-term financial success of the
Company and enhancing stockholder value.

                  2. DEFINITIONS. For purposes of the Plan, the following terms
shall have the following meanings:

                          (a) "AFFILIATE" shall mean an affiliate within the
                  meaning of Rule 12b-2 under the Exchange Act.

                          (b) "CAUSE" shall mean, unless otherwise determined by
                  the Committee: (1) in the case where there is no employment or
                  consulting agreement between the optionee and the Company or
                  its Affiliates at the time of grant or where such an agreement
                  exists but does not define "cause" (or words of like import),
                  the optionee's dishonesty, fraud, insubordination, willful
                  misconduct, refusal to perform services, unsatisfactory
                  performance of services or material breach of any written
                  agreement between the optionee and the Company or its
                  Affiliates, or (2) in the case where there is an employment or
                  consulting agreement between the optionee and the Company or
                  its Affiliates at the time of grant which defines 'cause" (or
                  words of like import), the meaning ascribed to such term under
                  such agreement.

                          (c) "CHANGE IN CONTROL" shall be deemed to occur if:
                  (1) there shall be consummated (x) any consolidation or merger
                  of the Company in which the Company is not the continuing or
                  surviving corporation or pursuant to which shares of Common
                  Stock would be converted into cash, securities or other
                  property, other than a merger of the Company in which the
                  holders of the Common Stock immediately prior to the merger
                  have the same proportionate ownership of common stock of the
                  surviving corporation immediately after the merger, or (y) any
                  sale, lease, exchange or other transfer (in one transaction or
                  a series of related transactions) of all, or substantially
                  all, of the assets of the Company, (2) the stockholders of the
                  Company shall approve any plan or proposal for liquidation or
                  dissolution of the Company, or (3) any person (as such term is
                  used in Section 13(d) and 14 (d) (2) of the Exchange Act),
                  shall become the beneficial owner (within the meaning Rule
                  13d-3 under the Exchange Act) of forty percent (40%) or more
                  of the outstanding Common Stock, or (4) during any period of
                  two (2) consecutive years, individuals who at the beginning of
                  such period constitute the entire Board shall cease for any
                  reason to constitute a majority thereof unless the election,
                  or the nomination for election by the Company's stockholders,
                  of each new director was approved by a vote of at least
                  two-thirds of the directors then still in office who were
                  directors at the beginning of the period or were so approved.

                          (d) "CODE" shall mean the Internal Revenue Code of
                  1996, as amended.

                          (e) "COMMITTEE" shall mean, the committee, consisting
                  of at least two (2) directors, appointed by the Board from
                  time to time to administer the Plan or, if no such committee
                  is appointed, the Board.

                          (f) "DETRIMENTAL ACTIVITY" shall mean: (1) the
                  rendering of services for any organization or engaging
                  directly or indirectly in any business which is or becomes
                  competitive with the company or its Affiliates, or which
                  organization of business, or the rendering of services to such
                  organization or business, is or becomes otherwise prejudicial
                  to or in conflict with the interests of the company or its
                  Affiliates, (2) the disclosure to anyone outside the Company
                  or its Affiliates, or the use in other than the Company's or
                  its Affiliates' business, without prior written authorization
                  from the company's or its Affiliates' business, without prior
                  written authorization from the Company, of any confidential
                  information or material relating to the business of the
                  Company or its Affiliates, acquired by the optionee either
                  during or after employment or other service with the Company
                  or its Affiliates, (3) the failure or refusal to disclose
                  promptly and to assign to the Company or its Affiliates all
                  right, title and interest in any invention or idea, patentable
                  or not, made or conceived by the optionee during employment by
                  or other service with the Company or its Affiliates, relating
                  in any manner to the actual or anticipated business, research
                  or development work of the Company or its Affiliates or the
                  failure or refusal to do anything reasonably necessary to
                  enable the Company or its Affiliates to secure a patent where
                  appropriate in the United States and in other countries, or
                  (4) any attempt directly or indirectly to induce any employee
                  of the Company or its Affiliates to be employed or perform
                  services elsewhere or any attempt directly or indirectly to
                  solicit the trade or business of any current or prospective
                  customer, supplier or partner of the Company or its
                  Affiliates.

                          (g) "DISABILITY" shall mean, unless as otherwise
                  determined by the Committee or as provided in an employment
                  agreement, the inability of an optionee to perform the
                  customary duties of his or her employment or other service for
                  the Company or its Affiliates by reason of a physical or
                  mental incapacity which is expected to result in death or to
                  be of indefinite duration.

<Page>



                          (h) "EFFECTIVE DATE" shall mean the date on which the
                  Plan was adopted by the Board, subject to the approval of the
                  Company's stockholders within twelve (12) months of such date.

                          (i) "EXCHANGE ACT" shall mean the Securities Exchange
                  Act of 1934, as amended.

                          (j) "EXCHANGE TRANSACTION" shall mean a merger (other
                  than a merger of the Company in which the holders of Common
                  Stock immediately prior to the merger have the same
                  proportionate ownership of Common Stock in the surviving
                  corporation immediately after the merger), consolidation,
                  acquisition of property or stock, separation, reorganization
                  (other than a mere reincorporation or the creation of a
                  holding company) or liquidation of the Company, as a result of
                  which the stockholders of the Company receive cash, stock or
                  other property in exchange for or in connection with their
                  shares of Common Stock.

                          (k) "FAIR MARKET VALUE" as of any date shall mean,
                  unless otherwise required by the Code or other applicable law,
                  the closing sale price per share of Common Stock as published
                  by the principal national securities exchange on which the
                  Common Stock is traded on such date or, if there is no sale of
                  Common Stock on such date, the average of the bid and asked
                  prices on such exchange at the close of trading on such date,
                  or if shares of the Common Stock are not listed on a national
                  securities exchange on such date, the closing price or, if
                  none, the average of the bid and asked prices in the
                  over-the-counter market at the close of trading on such date,
                  or if the Common Stock is not traded on a national securities
                  exchange of the over-the-counter market, the value of a share
                  of the Common Stock on such date as determined in good-faith
                  by the Committee.

                          (l) "INCENTIVE STOCK OPTION" shall mean an option that
                  is intended to be an "incentive stock option" within the
                  meaning of Section 422 of the Code.

                          (m) "NON-QUALIFIED STOCK OPTION" shall mean an Option
                  that is not an Incentive Stock Option.

                          (n) "OPTION" shall mean an Incentive Stock Option or a
                  Non-Qualified Stock Option granted pursuant to the Plan.

                          (o) "SECURING ACT" shall mean the Securities Act of
                  1933, as amended.

                          (p) "SUBSIDIARY" shall mean any "subsidiary
                  corporation" of the Company within the meaning of Section
                  424(f) of the Code.

                          (q) "TEN PERCENT STOCKHOLDER" shall mean a person
                  owning, at the time of grant, stock possessing more than ten
                  percent (10%) of the total combined voting power of all
                  classes of stock of the Company or any parent or subsidiary
                  corporation within the meaning of Section 424 of the Code.

                  3.      ADMINISTRATION

                          (a) COMMITTEE. The Plan shall be administered and
                  interpreted by the Committee.

                          (b) AUTHORITY OF COMMITTEE. Subject to the limitations
                  of the Plan, the Committee, acting in its sole and absolute
                  discretion, shall have full power and authority to: (1) select
                  the persons to whom options shall be granted, (2) grant
                  Options to such persons and prescribe the terms and conditions
                  of such options to such persons and prescribe the terms and
                  conditions of such options (including, but not limited to, the
                  exercise and vesting conditions applicable thereto), (3)
                  interpret and apply the provisions of the Plan and of any
                  agreement or other instrument evidencing an Option, (4) carry
                  out any responsibility of duty specifically reserved to the
                  Committee under the Plan, and (5) make and all determinations
                  and interpretations and take such other actions as may be
                  necessary or desirable in order to carry out the provisions,
                  intent and purposes of the Plan. A majority of the members of
                  their committee shall constitute a quorum. The committee may
                  act by the vote of a majority of its members present at a
                  meeting at which there is a quorum or by unanimous written
                  consent. The determinations of the Committee, including with
                  regard to questions of construction, interpretation and
                  administration, shall be final, binding and conclusive on all
                  persons.

                          (c) INDEMNIFICATION. The Company shall indemnify and
                  hold harmless each member of the committee and the Board and
                  any employee of the Company who provides assistance with the
                  administration of the Plan from and against any loss, cost,
                  liability (including any sum paid in settlement of a claim
                  with the approval of the Board), damage and expense (including
                  the advancement of reasonable legal and other expenses
                  incident thereto) arising out of or incurred in connection
                  with the Plan, unless and except to the extent attributable to
                  such person's fraud or willful misconduct.

                  4. ELIGIBILITY. Options may be granted under the Plan to any
member of the Board (whether or not an employee of the Company or its
Affiliates), to any officer or other employee of the Company or its Affiliates
and to any consultant or other independent contractor who performs or will
perform services for the Company or its Affiliates. Notwithstanding the
foregoing, Incentive Stock Options may only be granted to persons who are
employed by the Company or a subsidiary at the time of grant.

                  5. AVAILABLE SHARES. Subject to adjustment as provided in
Section10, (a) the maximum number of shares of Common Stock that may be issued
under the Plan shall not exceed 1,500,000 shares, and the (b) maximum number of
shares of Common Stock with respect to which

<Page>

Options may be granted to any employee of the Company or its Affiliates in any
calendar year shall not cover more than 200,000 shares. Shares of Common Stock
available for issuance under the plan may be either authorized and unissued or
held by the Company in its treasury. New options may be granted under the Plan
with respect to Shares of Common Stock which are covered by the unexercised
portion of an Option which has terminated or expired by its terms, by
cancellation or otherwise. No fractional shares of Common Stock may be issued
under the Plan.

                  6.      DISCRETIONARY STOCK OPTIONS.

                          (a) TYPE OF OPTIONS. Subject to the provisions hereof,
                  the Committee may grant Incentive Stock Options and Non-
                  Qualified Stock Options to eligible personnel upon which terms
                  and conditions as the Committee deems appropriate.

                          (b) OPTION TERM. Unless sooner terminated, all Options
                  shall expire not more than ten (10) years after the date the
                  Option is granted (or, in the case of an Incentive Stock
                  Option granted to a Ten Percent Stockholder, not more than
                  five (5) years).

                          (c) EXERCISE PRICE. The exercise price per share of
                  Common Stock covered by a Non-Qualified Stock Option may not
                  be less than the par value of a share of Common Stock on the
                  date the Option is granted. The exercise price per share of
                  Common Stock covered by an Incentive Stock Option may not be
                  less than one hundred percent (100%) of the Fair Market Value
                  of a share of Common Stock on the date the Option is granted
                  one hundred ten percent (110%) in case of an optionee who is a
                  Ten Percent Stockholder).

                          (d) EXERCISE OF OPTIONS. The Committee may establish
                  such vesting and other conditions and restrictions on the
                  exercise of an Option and/or upon the issuance of Common Stock
                  in connection with the exercise of an Option as it deems
                  appropriate. All or part of the exercisable portion of an
                  Option may be exercised at any time during the Option term,
                  except that, without the consent of the Committee, no partial
                  exercise of an option may be for less than one hundred (100)
                  shares.

                          (e) PAYMENT OF EXERCISE PRICE. An Option may be
                  exercised by transmitting to the Company: (i) a written notice
                  specifying the number of shares to be purchased, and (ii)
                  payment of the exercise price, together with the amount, if
                  any, deemed necessary by the Committee to enable the Company
                  to satisfy its federal, state, foreign or other tax
                  withholding obligations with respect to such exercise. The
                  Committee may establish such rules and procedures as it deems
                  appropriate for the exercise of Options. The exercise price of
                  shares of Common Stock acquired pursuant to the exercise of an
                  Option may be paid in cash, certified or bank check and/or
                  such other form of payment as may be permitted by the
                  Committee from time to time, including, without limitation,
                  shares of common Stock which have been owned by the holder for
                  at least six (6) months (free and clear of any liens and
                  encumbrances).

                  7. NON-TRANSFERABILITY. No Option shall be transferable by an
optionee other than upon the optionee's death to a beneficiary designated by the
optionee, or, if no designated beneficiary shall survive the optionee, pursuant
to the optionee's will or by the laws of descent and distribution. All Options
shall be exercisable during an optionee's lifetime only by the optionee. Any
attempt to transfer any Option shall be void, and no such Option shall in any
manner be liable for or subject to the debts, contracts, liabilities,
engagements or torts of any person who shall be entitled to such Option, nor
shall it be subject to attachment or legal process for or against such person.
Notwithstanding the foregoing, the Committee may, in its sole discretion, permit
an optionee to transfer a Non-Qualified Stock Option, in whole or in part, to
such persons and/or entities as are approved by the Committee from time to time
and subject to such terms and conditions as the Committee may determine from
time to time, including, without limitation, such terms and conditions as are
necessary or desirable to comply with applicable law.

                  8. EFFECT OF TERMINATION OF EMPLOYMENT OR OTHER SERVICE.
Except as otherwise provided herein or determined by the Committee, the
following rules shall apply with regard to Options held by an optionee at the
time of his or her termination of employment or other service with the Company
and its Affiliates:

                          (a) TERMINATION DUE TO DEATH OR DISABILITY. If an
                  optionee's employment or other service terminates due to his
                  or her death or Disability (or if the optionee's employment or
                  other service is terminated by reason of his or her Disability
                  and the optionee dies within one year of such termination of
                  employment or other service), then: (i) that portion of an
                  Option that is not exercisable on the date of termination
                  shall immediately terminate, and (ii) that portion of an
                  Option that is exercisable on the date of termination shall
                  remain exercisable, to the extent exercisable on the date of
                  termination, by the optionee (or the optionee's designated
                  beneficiary or representative) during the one year period
                  following the date of termination (or, during the one year
                  after the later death of a disabled optionee) or, if sooner,
                  until the expiration of the stated term thereof, and, to the
                  extent not exercised during such period, shall thereupon
                  terminate.

                          (b) TERMINATION FOR CAUSE OR AT A TIME WHEN CAUSE
                  EXISTS. If an optionee's employment or other service is
                  terminated by the Company or an Affiliate for Cause or if, at
                  the time of his or her termination, grounds for a termination
                  for Cause exist, then any option held by the optionee (whether
                  or not then exercisable) shall immediately terminate and cease
                  to be exercisable.

                          (c) OTHER TERMINATION. If an optionee's employment or
                  other service terminates for any reason or no reason, then,
                  except as provided for in an employment agreement: (i) that
                  portion of an Option held by the optionee that is not
                  exercisable on the date of termination shall immediately
                  terminate, and (ii) that portion of an Option that is
                  exercisable on the date of termination shall remain
                  exercisable, to the extent exercisable on the date of
                  termination, by the optionee during the ninety (90) day period
                  following the date of termination or, if sooner, until the
                  expiration of the stated term thereof, and, to the extent not
                  exercised during such period, shall thereupon terminate.

<Page>

                  9. CANCELLATION AND RESCISSION OF OPTIONS. Unless an Option
agreement specifies otherwise, the Committee may cancel, rescind, suspend,
withhold or otherwise limit or restrict any unexpired Option at any time if the
optionee is not in compliance with all applicable provisions of the award
agreement and the Plan, or if the optionee engages in a Detrimental Activity.
Upon exercise of an Option, the optionee shall certify in a manner acceptable to
the Company that he or she is in compliance with the terms and conditions of the
Plan and has not engaged in any Detrimental Activities. In the event an optionee
engages in any Detrimental Activity prior to, or during the six (6) months
after, any exercise, such exercise may be rescinded within two (2) years
thereafter. In the event of any such rescission, the optionee shall pay to the
Company the amount of any gain realized as a result of the rescinded exercise,
in such manner and on such terms and conditions as may be required, and the
Company and its Affiliates shall be entitled to set-off against the amount of
any such gain, any amount owed to the optionee by the Company or its Affiliates.

                  10.     CAPITAL CHANGE; REORGANIZATION; SALE.

                          (a) ADJUSTMENTS UPON CHANGES IN CAPITALIZATION. The
                  aggregate number and class of shares which may be issued under
                  the Plan, the maximum number and class of shares with respect
                  to which an option may be granted to any employee during any
                  calendar year and the number and class of shares and the
                  exercise price per share in effect under each outstanding
                  Option shall all be adjusted proportionately for any increase
                  or decrease in the number of issued shares of Common Stock
                  resulting from a split-up or consolidation of shares or any
                  like capital adjustment, or the payment of any stock dividend.

                          (b) CASH, STOCK OR OTHER PROPERTY FOR STOCK. Except as
                  otherwise provided in this subparagraph, in the event of an
                  Exchange Transaction, all optionee shall be permitted to
                  exercise their outstanding Options (whether or not otherwise
                  exercisable) at least fifteen (15) days prior to the Exchange
                  Transaction (and the Board shall notify each optionee of such
                  acceleration at least fifteen (15) days prior to the Exchange
                  Transaction) and any outstanding Options not exercised before
                  the consummation of the Exchange Transaction shall thereupon
                  terminate. Notwithstanding the preceding sentence, if, as a
                  part of the Exchange Transaction, the stockholders of the
                  Company receive capital stock of another corporation
                  ("Exchange Stock"), and if the Board, in its sole discretion,
                  so directs, then all outstanding Options shall be converted
                  into Options to purchase shares of Exchange Stock. The amount
                  and price of the converted options shall be determined by
                  adjusting the amount and price of the Options granted
                  hereunder on the same basis as the determination of the number
                  of shares of Exchange Stock the holders of Common Stock shall
                  receive in the Exchange Transaction.

                          (c) FRACTIONAL SHARES. In the event of any adjustment
                  in the number of shares covered by an Option, any fractional
                  shares resulting from such adjustment shall be disregarded,
                  and each such Option shall cover only the number of full
                  shares resulting from the adjustment.

                          (d) DETERMINATION OF BOARD TO BE FINAL. All
                  adjustments under this Section 10 shall be made by the Board,
                  and its determination as to what adjustments shall be made,
                  and the extent thereof, shall be final, binding and
                  conclusive.

                  11. RIGHTS AS A STOCKHOLDER. No shares of Common Stock shall
be issued in respect of the exercise of an Option until full payment therefor
has been made, and the applicable income tax withholding obligation has been
satisfied. The shares covered by the Option until the date a stock certificate
(or an equivalent) for such shares is issued to the holder. Except as otherwise
provided herein, no adjustments shall be made for dividend distributions or
other rights for which the record date is prior to the date such stock
certificate (or an equivalent) is issued.

                  12. TAX WITHHOLDING. As a condition to the exercise of any
Option or the lapse of restrictions on any shares of Common Stock, or in
connection with any other event under the Plan that gives rise to a federal or
other governmental tax withholding obligation on the part of the Company or its
Affiliates: (a) the Company may deduct or withhold (or cause to be deducted or
withheld) from any payment or distribution to an optionee whether or not
pursuant to the Plan, and (b) the Company shall be entitled to require that the
optionee remit cash to the Company (through payroll deduction or otherwise), in
each case in an amount sufficient in the opinion of the Company to satisfy such
withholding obligation. If the event giving rise to the withholding obligation
involves a transfer of shares of Common Stock, then, unless the applicable
agreement provides otherwise, at the discretion of the Committee, the optionee
may satisfy the withholding obligation described under this Section 12 by
electing to have the Company withhold shares of Common Stock (which withholding
shall be at a rate not in excess of the statutory minimum rate) or by tendering
previously owned shares of Common Stock, in each case having a Fair Market Value
equal to the amount of tax to be withheld (or by any other mechanism as may be
required to appropriate to conform with local tax and other rules).

                  13. AMENDMENT AND TERMINATION. The Board may amend or
terminate the Plan at any time, provided that no such action may adversely
affect the rights of the holder of any outstanding Option without his or her
consent. Except as otherwise provided in Section 10, any amendment which
increases the aggregate number of shares of Common Stock that may be issued
under the Plan, modifies the class of employees eligible to receive Options
under the Plan or otherwise requires stockholder approval shall, to the extent
required by applicable law, be subject to the approval of the Company's
stockholders. The Committee may amend the terms of any agreement or certificate
made or issued hereunder at any time from time to time provided that any
amendment which would adversely affect the rights of the holder may not be made
without his or her consent.

                  14. TERM OF THE PLAN. The Plan shall be effective on the
Effective Date. The Plan will terminate on the tenth anniversary of the
Effective Date, unless sooner terminated by the Board. The rights of any person
with respect to an Option granted under the Plan that is outstanding at the time
of the termination of the plan shall not be affected solely by reason of the
termination of the Plan and shall continue in accordance with the terms of the
Option (as then in effect or thereafter amended) and the Plan.

<Page>

                  15.     MISCELLANEOUS

                          (a) DOCUMENTATION. Each Option granted made under the
                  Plan shall be evidenced by a written agreement or other
                  written instrument the terms of which shall be established by
                  the Committee. To the extent not inconsistent with the
                  provisions of the Plan, the written agreement or other
                  instrument evidencing an Option shall govern the rights and
                  obligations of the optionee (and any person claiming through
                  the optionee) with respect to the Option.

                          (b) NO RIGHTS CONFERRED. Nothing contained herein
                  shall be construed to confer upon any individual any right to
                  be retained in the employ or other service of the Company or
                  its Affiliates or to interfere with the right of the Company
                  or its Affiliates to terminate an optionee's employment or
                  other services at any time.

                          (c) GOVERNING LAW. The Plan shall be governed by the
                  laws of the State of Delaware, without regard to its
                  principles of conflicts of law.

                          (d) DECISIONS AND DETERMINATIONS. All decisions or
                  determinations made by the Board and, except to the extent
                  rights or powers under the Plan are reserved specifically to
                  the discretion of the Board, all decisions and determinations
                  of the Committee, shall be final, binding and conclusive.

                          (e) SEVERABILITY. In the event any provision of the
                  Plan shall be held illegal or invalid for any reason, the
                  illegality or invalidity shall not affect the remaining parts
                  of the Plan, and the Plan shall be construed and enforced as
                  if the illegal or invalid provision had not been included.

                          (f) REQUIREMENTS OF LAW. The grant of Options and
                  issuance of shares under the Plan shall be subject to
                  compliance with all applicable laws, rules, and regulations,
                  and to such approvals by any governmental agencies or national
                  securities exchanges as the Committee deems necessary or
                  desirable.

                          (g) LISTING AND OTHER CONDITIONS. As long as the
                  Common Stock is listed on a national securities exchange or
                  system sponsored by a national securities association, the
                  issue of any shares of Common Stock pursuant to an Option
                  shall be conditioned upon such shares being listed on such
                  exchange or system. If at any time counsel to the Company
                  shall be of the opinion that any sale or delivery of shares of
                  Common Stock pursuant to an Option is or may in the
                  circumstances be unlawful or result in the imposition of
                  excise taxes on the Company under the statutes, rules or
                  regulations of any applicable jurisdiction, the Company shall
                  have no obligation to make such sale or delivery, or to may
                  any application or to effect or to maintain any qualification
                  or registration under the Securities Act or otherwise with
                  respect to shares of Common Stock or Options, and the right to
                  exercise any Option shall be suspended until, in the opinion
                  of said counsel, such sale or delivery shall be lawful or
                  shall not result in the imposition of excise taxes on the
                  Company.