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Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
OF
ANIMAS CORPORATION Animas Corporation (the Corporation), a corporation organized and existing under the laws of
the State of Delaware, hereby certifies as follows: A. The name of the Corporation is Animas Corporation. The Corporations original Certificate
of Incorporation was filed with the Secretary of State of the State of Delaware on July 9, 1996. B. This Amended and Restated Certificate of Incorporation, which amends and restates the
Amended and Restated Certificate of Incorporation in its entirety, was duly adopted in accordance
with Sections 242 and 245 of the Delaware General Corporation Law (the DGCL) by written consent
of the stockholders in accordance with Section 228 of the DGCL. C. The Amended and Restated Certificate of Incorporation of the Corporation shall read in its
entirety as follows: FIRST: Name: The name of the Corporation is Animas Corporation. SECOND: Registered Office. The address of the Corporations registered office in the
State of Delaware is Corporation Trust Center, 1209 Orange Street, County of New Castle, City of
Wilmington, State of Delaware 19801. The name of its registered agent at such address is The
Corporation Trust Company. THIRD: Purposes. The nature of the business or purposes of the Corporation to be
conducted or promoted is to engage in any lawful act or activity for which corporations may be
organized under the General Corporation Law of the State of Delaware and to do all things and
exercise all powers, rights and privileges that a business corporation may now or hereafter be
organized or authorized to do or to exercise under the laws of the State of Delaware. FOURTH: Capital. A. Authorized Shares. 1. General. The total number of shares of all classes of stock which the Corporation
shall have the authority to issue is 110,000,000 shares, of which 100,000,000 shares shall be
Common Stock, $0.01 par value per share, and 10,000,000 shares shall be Preferred Stock, $0.01 par
value per share. The number of authorized shares of any of the Common Stock or the Preferred Stock
may be increased or decreased (but not below the number of shares thereof then outstanding) by the
affirmative vote of the holders of a majority in voting power of the stock of the Corporation
entitled to vote thereon irrespective of the provisions of Section 242(b)(2) of the DGCL (or any
successor provision thereto), and no vote of the holders of any of the Common Stock or the
Preferred Stock voting separately as a class shall be required therefor. 2. Common Stock. (A) Dividends. Subject to the preferential rights, if any, of the holders of Preferred
Stock, the holders of Common Stock shall be entitled to receive, when, as and if declared by the
Board of Directors, out of the assets of the Corporation which are by law available therefor,
dividends payable either in cash, in property or in shares of capital stock. (B) Voting Rights. At every annual or special meeting of stockholders of the Corporation,
every share of Common Stock shall entitle the holder thereof to one vote, in person or by proxy,
for each share of Common Stock standing in his or her name on the books of the Corporation;
provided that, the holders of Common




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Stock shall have no voting rights with respect to matters reserved (by law or by agreement
with the Corporation) solely for any other class of capital stock. (C) Liquidation, Dissolution or Winding Up. In the event of any voluntary or involuntary
liquidation, dissolution or winding up of the affairs of the Corporation (a Liquidation), after
payment or provision for payment of the debts and other liabilities of the Corporation and of the
preferential amounts, if any, to which the holders of Preferred Stock shall be entitled, the
holders of all outstanding shares of Common Stock shall be entitled to receive the remaining assets
of the Corporation available for distribution to holders of Common Stock ratably in proportion to
the number of shares held by each such stockholder. 3. Preferred Stock. The Board of Directors is hereby expressly authorized, by
resolution or resolutions, to provide, out of the unissued shares of Preferred Stock, for series of
Preferred Stock and, with respect to each such series, to fix the number of shares constituting
such series and the designation of such series, the voting powers (if any) of the shares of such
series, and the preferences and relative, participating, optional or other special rights, if any,
and any qualifications, limitations or restrictions thereof, of the shares of such series. The
powers, preferences and relative, participating, optional and other special rights of each series
of Preferred Stock, and the qualifications, limitations or restrictions thereof, if any, may differ
from those of any and all other series at any time outstanding. B. Voting Powers. 1. Cumulative Voting. Then shall be no cumulative voting rights. 2. Voting by Ballot. Elections of directors need not be by ballot unless the Bylaws
of the Corporation provide otherwise. C. Preemptive Rights. The holders of the Common Stock shall have no preemptive rights
to subscribe for any shares of any class of stock of the Corporation whether now or hereafter
authorized. D. Consideration for Shares; Assessibility. The Board of Directors, from time to
time, may issue and sell the authorized shares of stock of the Corporation for such consideration
(not less than the par value thereof), upon such terms and in such manner as it may determine. Any
and all shares so issued, the full consideration for which shall have been paid or delivered, shall
be fully paid and nonassessable, and the holders thereof shall not be liable to the Corporation or
its creditors for any further payment thereon. FIFTH: Bylaws. In furtherance and not in limitation of the powers conferred by the
DGCL, the Board of Directors is expressly authorized to make, amend, alter and repeal the Bylaws of
the Corporation without the assent or vote of the stockholders, in any manner not inconsistent with
the laws of the State of Delaware or this Amended and Restated Certificate of Incorporation of the
Corporation. Notwithstanding anything to the contrary contained in this Amended and Restated
Certificate of Incorporation, the affirmative vote of the holders of at least 80 percent in voting
power of all the shares of the Corporation entitled to vote generally in the election of directors,
voting together as a single class, shall be required in order for the stockholders of the
Corporation to alter, amend or repeal the Bylaws or to adopt any provision inconsistent therewith
or with this Article FIFTH, Article SIXTH, Article SEVENTH or Article ELEVENTH of this Amended and
Restated Certificate of Incorporation. SIXTH: Board of Directors. A. Additional Powers of Board of Directors. In furtherance, and not in limitation, of
the powers conferred by the laws of the State of Delaware, the Board of Directors is expressly
authorized and empowered: 1. to make, alter, amend and repeal the Bylaws, subject to the power of the stockholders to
alter or repeal the Bylaws made by the Board of Directors; -2-




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2. without the assent or vote of the stockholders, to authorize and issue obligations of the
Corporation, secured or unsecured, to include therein such provisions as to redeemability,
convertability or otherwise, as the Board of Directors in its sole discretion may determine, and to
authorize the mortgaging or pledging, as security therefor, of any property of the Corporation,
real or personal, including after-acquired property; 3. in addition to the powers and authorities expressly conferred upon it hereby or by statute,
the Board of Directors may exercise all such powers and do all such acts and things as may be
exercised or done by the Corporation, subject, nevertheless, to the provisions of the laws of the
State of Delaware, this Amended and Restated Certificate of Incorporation and the Bylaws of the
Corporation. B. Composition of Board of Directors. The business and affairs of the Corporation
shall be managed by or under the direction of a Board of Directors consisting of not less than
three directors or more than fifteen directors, the exact number of directors to be determined from
time to time by resolution adopted by affirmative vote of a majority of the Board of Directors.
The directors shall be divided into three classes designated Class I, Class II and Class III. Each
class shall consist, as nearly as possible, of one-third of the total number of directors
constituting the entire Board of Directors. Class I directors shall be originally elected for a
term expiring at the succeeding annual meeting of stockholders, Class II directors shall be
originally elected for a term expiring at the second succeeding annual meeting of stockholders, and
Class III directors shall be originally elected for a term expiring at the third succeeding annual
meeting of stockholders. At each succeeding annual meeting of stockholders beginning in 2005,
successors to the class of directors whose term expires at that annual meeting shall be elected for
a term expiring at the third succeeding annual meeting of stockholders. If the number of directors
is changed, any increase or decrease shall be apportioned among the classes so as to maintain the
number of directors in each class as nearly equal as possible, and any additional director of any
class elected to fill a newly created directorship resulting from an increase in such class shall
hold office for a term that shall coincide with the remaining term of that class, but in no case
shall a decrease in the number of directors remove or shorten the term of any incumbent director.
A director shall hold office until the annual meeting for the year in which his term expires and
until his successor shall be elected and shall qualify, subject, however, to prior death,
resignation, retirement, disqualification or removal from office. C. Removal. Directors may be removed only for cause, and only by the affirmative vote
of at least 80 percent in voting power of all shares of the Corporation entitled to vote generally
in the election of directors, voting as a single class. Notwithstanding the foregoing, whenever
the holders of any one or more series of Preferred Stock issued by the Corporation shall have the
right, voting separately as a series or separately as a class with one or more such other series,
to elect directors at an annual or special meeting of stockholders, the election, term of office,
removal, filling of vacancies and other features of such directorships shall be governed by the
terms of this Amended and Restated Certificate of Incorporation (including any certificate of
designations relating to any series of Preferred Stock) applicable thereto, and such directors so
elected shall not be divided into classes pursuant to this Article unless expressly provided by
such terms. D. Vacancies. Unless the Board of Directors otherwise determines, and subject to the
rights of the holders of any series of Preferred Stock, newly created directorships resulting from
any increase in the authorized number of directors or any vacancies on the Board of Directors
resulting from death, resignation, retirement, disqualification, removal from office or other cause
may be filled only by a majority vote of the directors then in office, though less than a quorum,
and shall not be filled by the stockholders unless there are no directors remaining on the Board of
Directors. Any director so chosen (a vacancy director) shall be a director of the same class as
the director whose vacancy he or she fills. Such vacancy director shall hold office until the
annual meeting of stockholders at which the director whose vacancy he or she filled would have been
up for reelection, and until his or her successor shall have been elected and qualified. The
stockholders shall thereupon elect a director to fill the vacancy having been temporarily filled by
the vacancy director, which individual may include the incumbent vacancy director. The director so
elected shall be a director of the same class as the vacancy director and shall serve until the
annual meeting of stockholders at which the term of office of such class expires and until such
directors successor shall have been duly elected and qualified. SEVENTH: Meetings of Stockholders. Any action required or permitted to be taken by
the holders of the Common Stock of the Corporation must be effected at a duly called annual or
special meeting of such holders and may not be effected by any consent in writing by such holders.
Except as otherwise required by law and subject -3-




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to the rights of the holders of any series of Preferred Stock, special meetings of the
stockholders of the Corporation may be called only by the Chairman of the Board of Directors or the
Board of Directors pursuant to a resolution approved by the Board of Directors. EIGHTH: Personal Liability of Director or Officer. No director or officer of the
Corporation shall be personally liable to the Corporation or to any stockholder of the Corporation
for monetary damages for breach of fiduciary duty as a director or officer, provided that this
provision shall not limit the liability of a director or officer (i) for any breach of the
directors or the officers duty of loyalty to the Corporation or its stockholders, (ii) for acts
or omissions not in good faith or which involve intentional misconduct or a knowing violation of
law, (iii) under Section 174 of the General Corporation Law of Delaware, or (iv) for any
transaction from which the director or officer derived an improper personal benefit. Neither the
amendment nor the repeal of this Article EIGHTH shall eliminate or reduce the effect thereof in
respect of any matter occurring, or any cause of action, suit or claim that, but for this Article
EIGHTH would accrue or arise, prior to such amendment or repeal. NINTH: Indemnification, Advancement of Expenses, Non-Exclusivity of Rights. A. Indemnification of Directors, Officers, Employees or Agents. Each person who was
or is made a party or is threatened to be made a party to or is involved in any action, suit or
proceeding, whether civil, criminal, administrative or investigative in nature, including any
appeal, by reason of the fact that such person (or a person of whom such person is the legal
representative) is or was a director, officer, employee or agent of the Corporation or, while a
director, officer, employee or agent of the Corporation, is or was serving at the request of the
Corporation as a director, officer, trustee, partner, member, employee, other fiduciary or agent of
another corporation or of a partnership, joint venture, limited liability company, trust or other
enterprise, including service with respect to employee benefit plans or public service or
charitable organizations, whether the basis of such claim or proceeding is alleged actions or
omissions in any such capacity or in any other capacity while serving as a director, officer,
trustee, partner, member, employee, other fiduciary or agent thereof, shall be indemnified and held
harmless by the Corporation to the fullest extent permitted by the DGCL, against all expense and
liability (including without limitation, attorneys fees and disbursements, court costs, damages,
fines, amounts paid or to be paid in settlement, and excise taxes or penalties) reasonably incurred
or suffered by such person in connection therewith and such indemnification shall continue as to a
person who has ceased to be a director, officer, employee or agent of the Corporation and shall
inure to the benefit of such persons heirs, executors and administrators. The Corporation, by
provisions in its Bylaws or by agreement, shall accord to any current or former director, officer,
employee or agent of the Corporation the right to, or regulate the manner of providing to any
current or former director, officer, employee or agent of the Corporation, indemnification to the
fullest extent permitted by the DGCL. B. Advance of Expenses. The Corporation to the fullest extent permitted by the DGCL
shall advance to any person who is or was a director, officer, employee or agent of the Corporation
(or to the legal representative thereof) any and all expenses (including, without limitation,
attorneys fees and disbursements and court costs) reasonably incurred by such person in respect of
any proceeding to which such person (or a person of whom such person is a legal representative) is
made a party or threatened to be made a party by reason of the fact that such person is or was a
director, officer, employee or agent of the Corporation or, while a director, officer, employee or
agent of the Corporation, is or was serving at the request of the Corporation as a director,
officer, trustee, partner, member, employee, other fiduciary or agent of another corporation or a
partnership, joint venture, limited liability company, trust or other enterprise, including service
with respect to employee benefit plans or public service or charitable organizations; provided,
however, that, to the extent the DGCL requires, the payment of such expenses in advance of the
final disposition of the proceeding shall be made only upon delivery to the Corporation of an
undertaking, by or on behalf of such person, to repay all amounts so advanced if it shall
ultimately be determined that such person is not entitled to be indemnified against such expense
under this Article NINTH or otherwise. The Corporation by provisions in its Bylaws or by agreement
shall accord any such person the right to, or regulate the manner of providing to any such person,
such advancement of expenses to the fullest extent permitted by the DGCL. C. Non-Exclusivity of Rights. Any right to indemnification and advancement of
expenses conferred as permitted by this Article NINTH shall not be deemed exclusive of any other
right which any person may have or hereafter acquire under any statute (including the DGCL), any
other provision of this Amended and -4-




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Restated Certificate of Incorporation of the Corporation, any agreement, any vote of
stockholders or the Board of Directors or otherwise. TENTH: Section 203 of the Delaware General Corporation Law. The Corporation elects to
be governed by Section 203 of the DGCL, Business Combinations With Interested Stockholders as
permitted under and pursuant to subsection (b) of Section 203 of the DGCL. ELEVENTH: Amendment. Notwithstanding anything to the contrary contained in this
Amended and Restated Certificate of Incorporation, the affirmative vote of the holders of at least
80 percent in voting power of all the shares of the Corporation entitled to vote generally in the
election of directors, voting together as a single class, shall be required to alter, amend or
repeal Article FIFTH, Article SIXTH, Article SEVENTH or this Article ELEVENTH or to adopt any
provision inconsistent therewith. TWELFTH: Insurance. The Corporation may maintain insurance, at its expense, to
protect itself and any director, officer, employee or agent of the Corporation or of another
corporation or a partnership, joint venture, limited liability company, trust or other enterprise
against any expense, liability or loss, whether or not the Corporation would have the power to
indemnify such person against such expense, liability or loss under the DGCL. THIRTEENTH: Creditors. Whenever a compromise or arrangement is proposed between the
Corporation and its creditors or any class of them and/or between the Corporation and its
stockholders or any clan of them, any court of equitable jurisdiction within the State of Delaware
may, on the application in a summary way of the Corporation or of any creditor or stockholder
thereof or on the application of any receiver or receivers appointed for the Corporation under the
provisions of Section 291 of Title 8 of the Delaware Code or on the application of trustees in
dissolution or of any receiver or receivers appointed for the Corporation under the provisions of
Section 279 of Title 8 of the Delaware Code, order a meeting of the creditors or class of
creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may
be, to be summoned in such manner as the said court directs. If a majority in number representing
three-fourths in value of the creditors or class of creditors, and/or of the stockholders or class
of stockholders of the Corporation, as the case may be, agree to any compromise or arrangement and
to any reorganization of the Corporation as a consequence of such compromise or arrangement, the
said compromise or arrangement and the said reorganization shall, if sanctioned by the court to
which the said application has been made, be binding on all of the creditors or class of creditors,
and/or on all the stockholders or class of stockholders, of the Corporation, as the case may be,
and also on the Corporation. IN WITNESS WHEREOF, the undersigned has caused this Amended and Restated Certificate of
Incorporation to be signed by of the Corporation on May 25, 2004. ANIMAS CORPORATION/s/ Katherine D. CrothallName:
    Katherine D. CrothallTitle:
    President and Chief Executive Officer -5-