S-3

QuickLinks -- Click here to rapidly navigate through this document

As filed with the Securities and Exchange Commission on October 12, 2004

Registration No. 333-

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

FORM S-3
REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933

ADVANCED MAGNETICS, INC.
(Exact name of registrant as specified in its charter)

Delaware (State or other jurisdiction of incorporation or organization)	04-2742593 (IRS Employer Identification No.)
61 Mooney Street Cambridge, MA 02138 (617) 497-2070 (Address, including zip code, and telephone number, including area code, of registrant's principal executive offices)
Jerome Goldstein President, Chief Executive Officer and Treasurer Advanced Magnetics, Inc. 61 Mooney Street Cambridge, MA 02138 (617) 497-2070 (Name, address, including zip code, and telephone number, including area code, of agent for service)

With a copy to:
William J. Curry, Esq.
Sullivan & Worcester LLP
One Post Office Square
Boston, MA 02109
(617) 338-2800

Approximate date of commencement of proposed sale to the public: From time to time or at one time after the effective date of this registration statement, as determined by the registrant.

        If the only securities being registered on this Form are being offered pursuant to dividend or interest reinvestment plans, please check the following box:    o

        If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box:    ý

        If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.    o

        If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.    o

        If delivery of the prospectus is expected to be made pursuant to Rule 434, please check the following box.    o

CALCULATION OF REGISTRATION FEE

Title of each class of securities to be registered(1)	Amount to be registered(2)	Proposed maximum offering price per unit(2)(3)	Proposed maximum aggregate offering price(2)(3)(4)	Amount of registration fee
Common Stock ($.01 par value)(5)
Preferred Stock ($.01 par value)(6)
Warrants(7)
Total	$50,000,000(1)	100%	$50,000,000(1)	$6,335

(1)

In no event will the aggregate initial offering price of the securities issued from time to time under this registration statement exceed $50,000,000. The aggregate amount of common shares registered hereunder is limited to that which is permissible under Rule 415(a)(4) under the Securities Act of 1933, as amended. The securities registered hereunder may be sold separately, together or as units with other securities registered hereunder. There are also being registered hereunder an indeterminate principal amount of each class of securities registered hereunder (the "underlying securities") as may be issuable, without separate consideration, (i) upon conversion, exercise or exchange of any other class of securities registered hereunder, to the extent such securities are by their terms convertible into or exercisable or exchangeable for the underlying securities, or (ii) pursuant to antidilution provisions of any other class of securities registered hereunder.

(2)

Not specified for each class pursuant to General Instruction II.D. to Form S-3.

(3)

The proposed maximum offering price per unit and the aggregate offering price per class of security will be determined from time to time by the registrant in connection with the issuance by the registrant of the securities registered hereunder.

(4)

Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(o) under the Securities Act of 1933, as amended.

(5)

Subject to note (1) above, there is being registered hereunder an indeterminate amount of common shares as may be sold from time to time.

(6)

Subject to note (1) above, there is being registered hereunder an indeterminate amount of preferred shares as may be sold from time to time.

(7)

Subject to note (1) above, there is being registered hereunder an indeterminate amount of warrants to acquire other classes of securities registered hereunder as may be sold from time to time.

THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(A) OF THE SECURITIES ACT OF 1933, AS AMENDED, OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME EFFECTIVE ON SUCH DATE AS THE SECURITIES AND EXCHANGE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(A), MAY DETERMINE.

The information in this prospectus is not complete and may be changed. We may not sell these securities until the registration statement filed with the Securities and Exchange Commission is effective. This prospectus is not an offer to sell these securities and we are not soliciting an offer or offers to buy these securities in any state where the offer or sale is not permitted.

SUBJECT TO COMPLETION: DATED OCTOBER 12, 2004

PROSPECTUS

$50,000,000

Common Stock
Preferred Stock
Warrants

        We may offer and sell, from time to time, in one or more offerings:

•

common stock,



•

preferred stock, and



•

warrants

        The securities we offer will have an aggregate public offering price of up to $50,000,000. We may offer and sell these securities separately or together in units with other securities described in this prospectus.

        We will indicate the particular securities we offer and their specific terms in a supplement to this prospectus. In each case we would describe the type and amount of securities we are offering, the initial public offering price and the other terms of the offering.

        Our common stock is listed on the American Stock Exchange under the symbol "AVM." We will make applications to list any shares of common stock sold pursuant to a supplement to this prospectus on the AMEX. We have not determined whether we will list any of the other securities we may offer on any exchange or over-the-counter market. If we decide to seek listing of any securities, the supplement will disclose the exchange or market.

Investing in our securities involves risks. See "Risk Factors" on page 3.

        Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

        Our principal executive office is at 61 Mooney Street, Cambridge, Massachusetts, and our telephone number is (617) 497-2070.

The date of this prospectus is                        , 2004

TABLE OF CONTENTS

	Page
About This Prospectus	1
Cautionary Note Regarding Forward-Looking Statements	1
Our Company	2
Risk Factors	3
Ratio of Combined Fixed Charges and Preference Dividends to Earnings	3
Use of Proceeds	3
Description of Our Common Stock	4
Description of Our Preferred Stock	4
Description of Our Warrants	5
Description of Certain Provisions of Delaware Law and Our Certificate of Incorporation and By-Laws	6
Plan of Distribution	8
Validity of the Offered Securities	10
Experts	10
Documents Incorporated by Reference	10
Where You Can Find More Information	11

ii

ABOUT THIS PROSPECTUS

        This prospectus is part of a registration statement we filed with the Securities and Exchange Commission, or the SEC, using a "shelf" registration process. Under this shelf process, we may sell any combination of the securities described in this prospectus from time to time in one or more offerings up to a total amount of proceeds of $50,000,000.

        This prospectus provides you only with a general description of the securities we may offer. Each time we sell securities, we will provide a prospectus supplement containing specific information about the terms of that offering. The prospectus supplement may also add to, update or change information contained in this prospectus. You should read both this prospectus and any prospectus supplement together with additional information described under the headings "Where You Can Find More Information" and "Documents Incorporated By Reference."

        You should rely only on the information incorporated by reference or provided in this document or any applicable prospectus supplement. We have not authorized anyone to provide you with different information. If anyone provides you with different or inconsistent information, you should not rely on it. We will not make an offer of these securities in any jurisdiction where it is unlawful. You should assume that the information in this prospectus, as well as the information we have previously filed with the SEC and incorporated by reference in this prospectus, is accurate only as of the date of the documents containing the information.

References in this prospectus to the terms "Advanced Magnetics," "company," "we," "our" or "us" or other similar terms mean Advanced Magnetics, Inc.

CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

        We have made and incorporated by reference statements in this document that constitute "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995 and federal securities laws. This section provides a "safe harbor" for forward-looking statements to encourage companies to provide prospective information about themselves so long as they identify these statements as forward-looking and provide meaningful cautionary statements identifying important factors that could cause actual results to differ from the projected results. All statements other than statements of historical fact we make in this prospectus or in any document incorporated by reference are forward-looking statements. These statements are based on management's beliefs and assumptions and on information currently available to management and use words such as "expect," "anticipate," "intend," "plan," "believe," "estimate," or similar expressions. Forward-looking statements include information concerning possible or assumed future results of operations, future product development and related clinical trials and statements regarding future research and development. Forward-looking statements reflect our current expectations and are subject to various known and unknown risks, uncertainties and other factors. Our actual results could differ materially from those anticipated in these forward-looking statements. Important factors that could cause these differences include, among others, those set forth below. For a more detailed discussion of some, but not all, of these factors, please read carefully the information discussed under "Risk Factors" in the applicable prospectus supplement to be provided with this prospectus as well as other factors which may be described from time to time in our filings with the SEC.

•

the timing and results of our product development program for our product candidates, including uncertainties relating to our ability to successfully complete the clinical development of our product candidates,



•

the timing and results of regulatory interactions regarding the clinical development of our product candidates and uncertainties relating to our ability to obtain regulatory approval to market and sell our product candidates,



•

our ability to continue to operate at commercial scale in compliance with applicable manufacturing requirements,

•

uncertainties relating to the variable nature of our product sales cycles,



•

our ability to compete successfully against our competitors and the acceptance of our products in the marketplace, and



•

other trends in competitive or economic conditions affecting our financial condition or results of operations not presently contemplated.

        These cautionary statements should not be construed by you to be exhaustive and they are made only as of the date of this prospectus. You should not rely upon forward-looking statements except as statements of our present intentions and of our present expectations, which may or may not occur. You should read these cautionary statements as being applicable to all forward-looking statements wherever they appear. We assume no obligation, except as specifically required by law and the rules of the SEC, to update the forward-looking statements or the reasons why actual results could differ from those projected in the forward-looking statements to reflect events or circumstances after the date hereof.

OUR COMPANY

This overview highlights information contained in certain documents incorporated by reference into this prospectus. This overview does not contain all of the information that you should consider before investing in our securities. You should read the entire prospectus and any applicable prospectus supplement carefully, including the "Risk Factors" section and the financial statements and the notes to those statements incorporated herein or therein by reference, before making an investment decision.

        Advanced Magnetics is a developer of superparamagnetic iron oxide nanoparticles used in pharmaceutical products. We are dedicated to the development and commercialization of our proprietary nanoparticle technology for use in therapeutic iron compounds to treat anemia as well as novel imaging agents to aid in the diagnosis of cardiovascular disease and cancer. Ferumoxytol, the next-generation product in our development pipeline, is currently in Phase III studies as an intravenous iron replacement therapeutic in anemic chronic kidney disease patients, whether or not on dialysis. Phase II clinical trials of ferumoxytol for use as a contrast agent in magnetic resonance angiography, also known as MRA, are currently ongoing. In June 2000, we received an approvable letter, subject to certain conditions, from the U.S. Food and Drug Administration, the FDA, for Combidex®, our investigational molecular imaging agent to aid in the non-invasive diagnosis of metastatic lymph nodes. During the quarter ended June 30, 2004, we submitted a response to the approvable letter and are in the process of providing the FDA with additional details underlying supporting data in the submission in order to provide a complete response to the approvable letter. Our liver contrast agent, Feridex I.V.®, is approved and marketed in Europe, Japan, the United States, Argentina, South Korea and Israel. Our oral contrast agent, GastroMARK®, used for delineating the bowel in magnetic resonance imaging, is approved and marketed in Europe and the United States.

        Advanced Magnetics was incorporated in Delaware in 1981. Our principal offices are located at 61 Mooney Street, Cambridge, MA 02138, and our telephone number is (617) 497-2070.

2

RISK FACTORS

        An investment in our securities involves a high degree of risk. In addition to the other information included in, or incorporated by reference into, this prospectus, you should carefully consider the risk factors in any applicable prospectus supplement when determining whether or not to purchase the securities offered under this prospectus and the prospectus supplement.

RATIO OF EARNINGS TO COMBINED FIXED CHARGES
AND PREFERENCE STOCK DIVIDENDS

        The following table sets forth our ratio of earnings to combined fixed charges and preference stock dividends for the periods indicated:

Fiscal Year Ended September 30,
1999	2000		2001		2002		2003	Nine Months Ended June 30, 2004
(a)	(b	)	(c	)	(d	)	157.9x	(e	)

(a)

Earnings in fiscal 1999 were inadequate to cover combined fixed charges and preference dividends. The coverage deficiency was approximately $4.4 million.

(b)

Earnings in fiscal 2000 were inadequate to cover combined fixed charges and preference dividends. The coverage deficiency was approximately $3.8 million.

(c)

Earnings in fiscal 2001 were inadequate to cover combined fixed charges and preference dividends. The coverage deficiency was approximately $3.8 million.

(d)

Earnings in fiscal 2002 were inadequate to cover combined fixed charges and preference dividends. The coverage deficiency was approximately $1.7 million.

(e)

Earnings in the nine months ended June 30, 2004 were inadequate to cover combined fixed charges and preference dividends. The coverage deficiency was approximately $2.3 million.

        The ratios above were computed by dividing earnings by combined fixed charges and preference dividends. We did not pay or accrue any preference dividends for the periods presented. For this purpose, earnings consist of (a) pre-tax income (loss) from continuing operations (which excludes the cumulative effect of accounting change) before adjustment for minority interests in consolidated subsidiaries or income (loss) from equity investees, and (b) fixed charges, including estimated interest associated with certain facility, equipment and vehicle leases. Fixed charges consist of that portion of rental expense associated with certain facility, equipment and vehicle leases considered to be a reasonable estimate of the interest factor.

USE OF PROCEEDS

        Unless otherwise described in a prospectus supplement, we intend to use the net proceeds from the sale of the offered securities for general corporate purposes, which may include, but are not limited to, working capital, ongoing research and development activities and capital expenditures. Pending any specific utilization, the proceeds from the sale of the offered securities may be invested in a manner designed to ensure levels of liquidity which correspond to our current and foreseeable cash needs. Such investments may include, but not be limited to, short-term investments, including government bonds, or other interest-bearing investments.

3

DESCRIPTION OF OUR COMMON STOCK

        We are authorized to issue up to 15,000,000 shares of common stock, $.01 par value per share.

        This section describes the general terms of our common stock that we may offer from time to time. For more detailed information, a holder of our common stock should refer to our certificate of incorporation and our by-laws, copies of which are filed with the SEC as exhibits to the registration statement of which this prospectus is a part.

        Holders of our common stock are entitled to one vote per share and vote together as a single class on all matters to be voted on by our stockholders. Pursuant to our certificate of incorporation, there are no cumulative voting rights in the election of directors. The approval of corporate actions may also require the approval of the holders of any series of our preferred stock. See "Description of Our Preferred Stock."

        Our common stock will be the only type of our capital stock entitled to vote in the election and removal of directors and other matters presented to our stockholders from time to time, unless we issue voting preferred stock or our certificate of incorporation or the law requires otherwise.

        Our common stockholders will be entitled to receive dividends and distributions declared by our board of directors, or board, to the extent permitted by outstanding series of preferred stock and by our certificate of incorporation. If a dividend is declared, it will be distributed pro rata to our common stockholders on a per share basis.

        If we are liquidated or dissolved, our common stockholders will be entitled to receive our assets and funds available for distribution to common stockholders in proportion to the number of shares they hold. Our common stockholders may not receive any assets or funds until our creditors have been paid in full and the preferential or participating rights of our preferred stockholders, if any, have been satisfied.

        Holders of our common stock will not have any preemptive, subscription or conversion rights with respect to shares of our common stock. We may issue additional shares of our common stock, if authorized by our board, without the common stockholders' approval, unless required by Delaware law or a stock exchange on which our securities are traded. The issuance of additional shares could have the effect of diluting any earnings per share and the book value per share of outstanding shares of common stock. If we receive the appropriate payment, shares of our common stock that we issue will be fully paid and nonassessable.

        Reference is made to the applicable prospectus supplement relating to the common stock offered by that prospectus supplement for specific terms, including:

•

amount and number of shares offered,



•

the initial offering price, if any, and market price, and



•

information with respect to dividends.

DESCRIPTION OF OUR PREFERRED STOCK

        We are authorized to issue up to 2,000,000 shares of preferred stock, $.01 par value per share.

        This section describes the general terms and provisions of our preferred stock that we may offer from time to time. The applicable prospectus supplement will describe the specific terms of the shares of preferred stock offered through that prospectus supplement. We will file a copy of the certificate of designation that contains the terms of each new series of preferred stock with the SEC each time we issue a new series of preferred stock, and these certificates of designation will be incorporated by reference into the registration statement of which this prospectus is a part. Each certificate of

4

designation will establish the number of shares included in a designated series and fix the designation, powers, privileges, preferences and rights of the shares of each series as well as any applicable qualifications, limitations or restrictions. A holder of our preferred stock should refer to the applicable certificate of designation, our certificate of incorporation and the applicable prospectus supplement for more specific information.

        Our board has been authorized, subject to limitations provided in our certificate of incorporation, to provide for the issuance of shares of our preferred stock in multiple series. As of the date of this prospectus, no series has been designated and no shares of our preferred stock are currently outstanding.

        With respect to each series of our preferred stock, our board has the authority to fix, among other things, the following terms:

•

the designation of the series,



•

the number of shares within the series,



•

whether the dividends are cumulative and, if cumulative, the dates from which dividends are cumulative,



•

the rate of any dividends, any conditions upon which dividends are payable, and the dates of payment of dividends,



•

whether the shares are redeemable, the redemption price and the terms of redemption,



•

the amount payable to a holder for each share owned if we are dissolved or liquidated,



•

whether the shares are convertible or exchangeable, the price or rate of exchange, and the applicable terms and conditions,



•

any restrictions on issuance of shares in the same series or any other series, and



•

the voting rights, if any, of the shares of the series.

        Holders of our preferred stock will not have preemptive rights with respect to shares of our preferred stock. In addition, rights with respect to shares of our preferred stock will be subordinate to the rights of our general creditors. If we receive the appropriate payment, shares of our preferred stock that we issue will be fully paid and nonassessable. The issuance of preferred stock could discourage an unsolicited acquisition proposal.

        We currently plan to retain American Stock Transfer & Trust Company as the registrar and transfer agent of any series of our preferred stock.

DESCRIPTION OF OUR WARRANTS

        This section describes the general terms and provisions of our warrants to acquire our securities that we may issue from time to time. The applicable prospectus supplement will describe the specific terms of the warrants offered through that prospectus supplement.

        We may issue warrants for the purchase of our common stock or preferred stock. We may issue warrants independently or together with other securities, and they may be attached to or separate from the other securities. Each series of warrants will be issued under a separate warrant agreement that we will enter into with American Stock Transfer & Trust Company, or another bank or trust company, as warrant agent, as detailed in the applicable prospectus supplement. The warrant agent will act solely as our agent in connection with the warrants and will not assume any obligation, or agency or trust relationship, with you. We will file a copy of the warrant and warrant agreement with the SEC each time we issue a series of warrants, and these warrants and warrant agreements will be incorporated by

5

reference into the registration statement of which this prospectus is a part. A holder of our warrants should refer to the provisions of the applicable warrant agreement and prospectus supplement for more specific information.

        The prospectus supplement relating to a particular issue of warrants will describe the terms of those warrants, including, where applicable:

•

the offering price,



•

the number of warrants offered,



•

the securities underlying the warrants,



•

the exercise price, the amount of securities you will receive upon exercise, the procedure for exercise of the warrants and the circumstances, if any, that will cause the warrants to be automatically exercised,



•

the rights, if any, we have to redeem the warrants,



•

the date on which the warrants will expire,



•

U.S. federal income tax consequences,



•

the name of the warrant agent, and



•

any other terms of the warrants.

        After your warrants expire they will become void. All warrants will be issued in registered form. The prospectus supplement may provide for the adjustment of the exercise price of the warrants.

        Warrants may be exercised at the appropriate office of the warrant agent or any other office indicated in the applicable prospectus supplement. Before the exercise of warrants, holders will not have any of the rights of holders of the securities purchasable upon exercise and will not be entitled to payments made to holders of those securities.

        The warrant agreements may be amended or supplemented without the consent of the holders of the warrants to which they apply to effect changes that are not inconsistent with the provisions of the warrants and that do not materially and adversely affect the interests of the holders of the warrants. However, any amendment that materially and adversely alters the rights of the holders of warrants will not be effective unless the holders of at least a majority of the applicable warrants then outstanding approve the amendment. Every holder of an outstanding warrant at the time any amendment becomes effective, by continuing to hold the warrant, will be bound by the applicable warrant agreement as amended. The prospectus supplement applicable to a particular series of warrants may provide that certain provisions of the warrants, including the securities for which they may be exercisable, the exercise price and the expiration date, may not be altered without the consent of the holder of each warrant.

DESCRIPTION OF CERTAIN PROVISIONS OF DELAWARE LAW
AND OUR CERTIFICATE OF INCORPORATION AND BY-LAWS

        We are organized as a Delaware corporation. The following is a summary of our certificate of incorporation and by-laws and certain provisions of the Delaware General Corporation Law, or the DGCL. Because it is a summary, it does not contain all the information that may be important to you. If you want more information, you should read our entire certificate of incorporation and by-laws, copies of which are filed with the SEC as exhibits to the registration statement of which this prospectus is a part, see "Where You Can Find More Information," or refer to the provisions of the DGCL.

6

Classification of Directors

        Our by-laws provide that, except as otherwise required by specific provisions of the certificate of incorporation relating to the rights of holders of any class or series of preferred stock to elect additional directors under specified circumstances, the number of our directors may be fixed from time to time by a resolution adopted by a majority of our board but must not be less than one. Our board is not classified into classes. A director may be removed, with or without cause, by the holders of a majority of the shares then entitled to vote at an election of directors, subject to the rights of any series of preferred stock then outstanding.

Special Meetings

        Except as otherwise required by law and subject to the rights of holders of any class or series of preferred stock, special meetings of the stockholders may only be called by our President or by our board. No business other than that stated in the notice of meeting may be transacted at any special meeting of stockholders.

Limitation of Liability and Indemnification

        Our certificate of incorporation provides that we shall indemnify our directors and officers to the fullest extent that Delaware law permits. Our certificate of incorporation also provides that we, by action of our board, may provide indemnification to our employees and agents with the same scope and effect as the indemnification of our officers and directors. Delaware law permits a corporation to indemnify any director, officer, employee or agent made or threatened to be made a party to any pending or completed proceeding if the person acted in good faith and in a manner that the person reasonably believed to be in the best interests of the corporation and, with respect to any criminal proceeding, had no reasonable cause to believe that his or her conduct was unlawful.

        Our certificate of incorporation limits the liability of our directors to the fullest extent permitted by the DGCL. The DGCL provides that directors will not be personally liable for monetary damages for breach of their fiduciary duties as directors, except liability for:

•

any breach of their duty of loyalty to the corporation or its stockholders,



•

acts or omissions not in good faith or which involve intentional misconduct or a knowing violation of law,



•

unlawful payments of dividends or unlawful stock repurchases or redemptions, or



•

any transaction from which the director derived an improper personal benefit.

        The effect of this provision may be to reduce the likelihood of derivative litigation against directors for breach of their duty of care, even though the action, if successful, might otherwise have benefited us and our stockholders. This provision has no effect on any non-monetary remedies that may be available to us or our stockholders, nor does it relieve us or our officers or directors from compliance with federal or state securities laws.

        Each of our directors is party to an indemnification agreement that provides specific contractual assurance that the indemnification protection promised by certificate of incorporation and by-laws will be available.

        As permitted by our certificate of incorporation, we have purchased and maintain insurance on behalf of our directors and officers for any expense, liability or loss incurred by them arising out of their actions in that capacity if we would have the power to indemnify such person against such expense, liability or loss under the DGCL.

7

Section 203 of the Delaware General Corporation Law

        Section 203 of the DGCL prohibits a defined set of transactions between a Delaware corporation, such as us, and an "interested stockholder." An interested stockholder is defined as a person who, together with any affiliates or associates of such person, beneficially owns, directly or indirectly, 15% or more of the outstanding voting stock of a Delaware corporation. This provision may prohibit business combinations between an interested stockholder and a corporation for a period of three years after the date the interested stockholder becomes an interested stockholder. The term "business combination" is broadly defined to include mergers, consolidations, sales or other dispositions of assets having a total value in excess of 10% of the consolidated assets of the corporation, and some other transactions that would increase the interested stockholder's proportionate share ownership in the corporation.

        This prohibition is effective unless:

•

either the business combination or the transaction that resulted in the interested stockholder becoming an interested stockholder is approved by our board prior to the time the interested stockholder becomes an interested stockholder,



•

the interested stockholder owns at least 85% of our voting stock, other than stock held by directors who are also officers or by qualified employee stock plans, upon completion of the transaction in which it becomes an interested stockholder, or



•

the business combination is approved by a majority of our board and by the affirmative vote of 66²/3% of the outstanding voting stock that is not owned by the interested stockholder.

        In general, the prohibitions do not apply to business combinations with persons who were interested stockholders prior to the corporation becoming subject to Section 203.

Stock Exchange Listing

        Our common stock is listed on the American Stock Exchange. The trading symbol for our common stock on this exchange is "AVM."

Transfer Agent

        American Stock Transfer & Trust Company is the transfer agent for our common stock.

PLAN OF DISTRIBUTION

        We may sell the securities in and outside the United States (a) through underwriters or dealers, (b) directly to purchasers, including our affiliates, (c) through agents or (d) through a combination of any of these methods. The applicable prospectus supplement will include the following information:

•

the terms of the offering,



•

the names of any underwriters or agents,



•

the name or names of any managing underwriter or underwriters,



•

the purchase price of the securities,



•

the net proceeds from the sale of the securities,



•

any delayed delivery arrangements,



•

any underwriting discounts, commissions and other items constituting underwriters' compensation,



•

any initial public offering price,

8

•

any discounts or concessions allowed or reallowed or paid to dealers, and



•

any commissions paid to agents.

        The sale of the securities may be effected in transactions (a) on any national or international securities exchange or quotation service on which the securities may be listed or quoted at the time of sale, (b) in the over-the-counter market, (c) in transactions otherwise than on such exchanges or in the over-the-counter market or (d) through the writing of options.

        The distribution of offered securities may be effected from time to time in one or more transactions at a fixed price or prices, which may be changed, at market prices prevailing at the time of sale, at prices related to the market prices, or at negotiated prices.

Sale Through Underwriters or Dealers

        If underwriters are used in the sale of any of these securities, the underwriters will acquire the securities for their own account. The underwriters may resell the securities from time to time in one or more transactions, including negotiated transactions, at a fixed public offering price or at varying prices determined at the time of sale. Underwriters may offer securities to the public either through underwriting syndicates represented by one or more managing underwriters or directly by one or more firms acting as underwriters. Unless we inform you otherwise in any prospectus supplement, the obligations of the underwriters to purchase the securities will be subject to certain conditions, and the underwriters will be obligated to purchase all the offered securities if they purchase any of them. We may grant underwriters an option to purchase additional securities to cover over-allotments, if any, in connection with the distribution. The underwriters may change from time to time any initial public offering price and any discounts or concessions allowed or reallowed or paid to dealers.

        During and after an offering through underwriters, the underwriters may purchase and sell the securities in the open market. These transactions may include overallotment and stabilizing transactions and purchases to cover syndicate short positions created in connection with the offering. The underwriters may also impose a penalty bid, which means that selling concessions allowed to syndicate members or other broker-dealers for the offered securities sold for their account may be reclaimed by the syndicate if the offered securities are repurchased by the syndicate in stabilizing or covering transactions. These activities may stabilize, maintain or otherwise affect the market price of the offered securities, which may be higher than the price that might otherwise prevail in the open market. If commenced, the underwriters may discontinue these activities at any time.

        Some or all of the securities that we offer though this prospectus may be new issues of securities with no established trading market. Any underwriters to whom we sell these securities for public offering and sale may make a market in those securities, but they will not be obligated to and they may discontinue any market making at any time without notice. Accordingly, we cannot assure you of the liquidity of, or continued trading markets for, any securities that we offer.

        If dealers are used in the sale of securities, we will sell the securities to them as principals. They may then resell those securities to the public at varying prices determined by the dealers at the time of resale. We will include in the prospectus supplement the names of the dealers and the terms of the transaction.

Direct Sales and Sales Through Agents

        We may sell the securities directly, and not through underwriters or agents. We may also sell the securities through agents designated from time to time. In the prospectus supplement, we will name any agent involved in the offer or sale of the offered securities, and we will describe any commissions payable to the agent. Unless we inform you otherwise in the prospectus supplement, any agent will agree to use its reasonable best efforts to solicit purchases for the period of its appointment.

9

        We may sell the securities directly to institutional investors or others who may be deemed to be underwriters within the meaning of the Securities Act of 1933, as amended, or the Securities Act, with respect to any sale of those securities. We will describe the terms of any such sales in the prospectus supplement.

        We may enter into derivative transactions with third parties, or sell securities not covered by this prospectus to third parties in privately negotiated transactions. If the applicable prospectus supplement indicates, in connection with those derivatives, the third parties may sell securities covered by this prospectus and the applicable prospectus supplement, including in short sale transactions. If so, the third party may use securities pledged by us or borrowed from us or others to settle those sales or to close out any related open borrowings of stock, and may use securities received from us in settlement of those derivatives to close out any related open borrowings of stock. The third party in such sale transactions will be an underwriter and, if not identified in this prospectus, will be identified in the applicable prospectus supplement (or a post-effective amendment).

Delayed Delivery Contracts

        If we so indicate in the prospectus supplement, we may authorize agents, underwriters or dealers to solicit offers from certain types of institutions to purchase securities from us at the public offering price under delayed delivery contracts. These contracts would provide for payment and delivery on a specified date in the future. The contracts would be subject only to those conditions described in the prospectus supplement. The prospectus supplement will describe the commission payable for solicitation of those contracts.

General Information

        We may have agreements with the agents, dealers and underwriters to indemnify them against certain civil liabilities, including liabilities under the Securities Act, or to contribute with respect to payments that the agents, dealers or underwriters may be required to make. Agents, dealers and underwriters may be customers of, engage in transactions with or perform services for us in the ordinary course of their businesses.

VALIDITY OF THE OFFERED SECURITIES

        Certain legal matters with respect to the securities offered hereby have been passed upon by Sullivan & Worcester LLP, Boston, Massachusetts. As of the date of this prospectus, certain attorneys with the firm of Sullivan & Worcester LLP beneficially own an aggregate of approximately 1,700 shares of our common stock.

EXPERTS

        The financial statements incorporated in this prospectus and elsewhere in this registration statement by reference to our Annual Report on Form 10-K for the year ended September 30, 2003 have been so incorporated in reliance on the report of PricewaterhouseCoopers LLP, independent registered public accounting firm, given on the authority of said firm as experts in auditing and accounting.

DOCUMENTS INCORPORATED BY REFERENCE

        The SEC allows us to "incorporate by reference" the information we file with it, which means that we can disclose important information to you by referring you to those documents. The information we incorporate by reference is considered part of this prospectus. Statements in this prospectus regarding the contents of any contract or other document may not be complete. You should refer to the copy of the contract or other document filed as an exhibit to the registration statement. Later information filed

10

with the SEC will update and supersede information we have included or incorporated by reference in this prospectus.

        We incorporate by reference the documents listed below, which have been filed with the SEC:

1.

Our Annual Report on Form 10-K for the fiscal year ended September 30, 2003,



2.

Our Quarterly Report on Form 10-Q for the fiscal quarter ended December 31, 2003,



3.

Our Quarterly Report on Form 10-Q for the fiscal quarter ended March 31, 2004,



4.

Our Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 2004,



5.

Our Current Report on Form 8-K as filed on November 20, 2003,



6.

Our Current Report on Form 8-K as filed on June 25, 2004,



7.

Our Current Report on Form 8-K as filed on July 12, 2004,



8.

Our Current Report on Form 8-K as filed on July 26, 2004, and



9.

The section entitled "Description of Registrant's Securities to be Registered" contained in our Registration Statement on Form 8-A as filed on September 24, 1991.

        We also incorporate by reference any filings made after the date of the initial filing of the registration statement of which this prospectus forms a part including filings made prior to the effectiveness of the registration statement, made with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934 until the offering of the securities made by this prospectus is completed or terminated.

        We will provide without charge to each person, including any beneficial owner, to whom this prospectus is delivered, upon the written or oral request of that person, a copy of any and all of the information that has been incorporated in this prospectus by reference other than exhibits unless those exhibits are specifically incorporated by reference into the documents. Requests for these copies should be directed to our Chief Financial Officer at the following address and telephone number: Advanced Magnetics, Inc., 61 Mooney Street, Cambridge, MA 02138; (617) 497-2070.

WHERE YOU CAN FIND MORE INFORMATION

        We file reports, proxy statements and other information with the SEC. You may read and copy the reports, proxy statements and other information that we file with the SEC at the SEC's Public Reference Room at 450 Fifth Street, N.W., Washington, D.C. 20549. Please call the SEC at 1-800-SEC-0330 for information about the operation of its Public Reference Room and for its prescribed rates to obtain copies of such material. The SEC also maintains an Internet site that contains reports, proxy and information statements and other information regarding registrants, like us, that file electronically with the SEC. The address of the SEC's Internet site is http://www.sec.gov. Our Internet site is http://www.advancedmagnetics.com. Information contained on these Internet sites is not a part of this prospectus.

        This prospectus provides you with a general description of the common stock, preferred stock and warrants being registered. This prospectus is part of a registration statement that we have filed with the SEC. To see more detail, you should read the registration statement and the exhibits and schedules filed with, or incorporated by reference into, our registration statement.

11

PART II
INFORMATION NOT REQUIRED IN PROSPECTUS

Item 14. Other Expenses of Issuance and Distribution.

        The following table sets forth the various expenses to be incurred in connection with the sale and distribution of the securities being registered hereby, all of which will be borne by Advanced Magnetics. All amounts shown are estimates except for the Securities and Exchange Commission registration fee:

Securities and Exchange Commission registration fee		$	6,335
Printing and Engraving Expenses		$	75,000
Legal fees and expenses		$	100,000
Accounting fees and expenses		$	10,000
Miscellaneous expenses		$	78,665
	Total	$	170,000

Item 15. Indemnification of Directors and Officers.

        Section 145 of the General Corporation Law of Delaware, or the DGCL, empowers a corporation to indemnify any person who was or is a party or is threatened to be made a party to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative, by reason of the fact that he or she is or was a director, officer, employee or agent of the corporation or another enterprise if serving at the request of the corporation. Depending on the character of the proceeding, a corporation may indemnify against expenses (including attorney's fees), judgments, fines and amounts paid in settlement actually and reasonably incurred in connection with such action, suit or proceeding if the person indemnified acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the best interests of the corporation, and, with respect to any criminal action or proceeding, had no reasonable cause to believe his or her conduct was unlawful. In the case of an action by or in the right of the corporation, no indemnification may be made in respect to any claim, issue or matter as to which such person shall have been adjudged to be liable to the corporation unless and only to the extent that the Court of Chancery or the court in which such action or suit was brought shall determine that despite the adjudication of liability, but in view of all the circumstances of the case, such person is fairly and reasonably entitled to indemnity for such expenses that the court shall deem proper. Section 145 further provides that to the extent a present or former director or officer of a corporation has been successful in the defense of any action, suit or proceeding referred to above, or in defense of any claim, issue or matter therein, he or she shall be indemnified against expenses (including attorney's fees) actually and reasonably incurred by him or her in connection therewith.

        The registrant's certificate of incorporation, as amended, provides that the registrant shall, to the fullest extent permitted by the DGCL, indemnify any director or officer which it shall have the power to indemnify under the DGCL against any expenses, liabilities, or other matters referred to in or covered by Section 145 of the DGCL. This indemnification continues after such person ceases to be a director or officer and inures to the benefit of the heirs, executors and administrators of said person. The registrant shall not be required to indemnify a person in connection with such action, suit or proceeding initiated by such person if it was not authorized by the registrant's Board of Directors except under limited circumstances. The certificate of incorporation also provides that the right to indemnification includes the right to be paid by the registrant for the expenses incurred in defending any such proceeding in advance of its final disposition; provided, however, that the payment of such expenses incurred by a director or officer in advance of the final disposition of a proceeding shall be made only upon delivery by the registrant of an undertaking, by or on behalf of such director or officer, to repay all amounts so advanced if it shall ultimately be determined that such director or

II-1

officer is not entitled to be indemnified under the certificate of incorporation or otherwise. The certificate of incorporation provides that the registrant, by action of its Board of Directors, may provide indemnification to employees and agents of the registrant with the same scope and effect as the indemnification of directors and officers. The certificate of incorporation also contains a provision eliminating the liability of directors of the registrant to the registrant or its stockholders for monetary damage, to the fullest extent permitted by law. The certificate of incorporation also permits the registrant to purchase and maintain insurance to protect itself and any director, officer, employee or agent against any expense, liability, or loss incurred by him or her if the registrant would have the power to indemnify such persons against such expense, liability or loss under the General Corporation Law of Delaware. The certificate of incorporation also permits the registrant to enter into agreements with any director, officer, employee or agent providing for indemnification rights equivalent to or greater than the indemnification rights set forth in the certificate of incorporation. The registrant has entered into indemnification agreements with all of its directors and maintains insurance for each director and executive officer.

        Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers or persons controlling the registrant pursuant to the foregoing provisions, the registrant has been informed that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Act and is therefore unenforceable.

Item 16. Exhibits.

        The following exhibits are filed as part of this registration statement:

Exhibit No.	Description of Documents
*1.1	Form of Underwriting Agreement (for Common Stock).
*1.2	Form of Underwriting Agreement (for Preferred Stock).
*1.3	Form of Underwriting Agreement (for Warrants).
+4.1	Certificate of Incorporation of the registrant, as amended.
+4.2	By-Laws of the registrant, as amended.
++4.3	Specimen certificate representing the registrant's Common Stock.
*4.4	Form of Certificate of Designation for the Preferred Stock.
*4.5	Form of Preferred Stock Certificate.
*4.6	Form of Warrant Agreement, including form of warrant.
*5.1	Opinion of Sullivan & Worcester LLP as to the legality of the securities being registered.
**10.1	Representative Form of Indemnification Agreement.
**12.1	Statement Regarding Computation of Ratio of Earnings to Combined Fixed Charges and Preference Stock Dividends.
**23.1	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm.
**23.2	Consent of Sullivan & Worcester LLP (included in Exhibit 5.1).
**24	Powers of Attorney (included in the signature pages of this registration statement).

+

Incorporated herein by reference the registrant's Annual Report on Form 10-K for the fiscal year ended September 30, 2000.

++

Incorporated by reference to Exhibit 6 to the Registration Statement on Form 8-A of the registrant, Reg. No. 1-10865.

*

To be filed by amendment or incorporated by reference in connection with the offering of any securities, as appropriate.

**

Filed herewith.

II-2

Item 17. Undertakings.

        The undersigned registrant hereby undertakes:

        (1)   To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

          (i)  To include any prospectus required by Section 10(a)(3) of the Securities Act of 1933;

         (ii)  To reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20 percent change in the maximum aggregate offering price set forth in the "Calculation of Registration Fee" table in the effective registration statement;

        (iii)  To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement;

provided, however, that paragraphs (1)(i) and (1)(ii) do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in periodic reports filed with or furnished to the Commission by the registrant pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in the registration statement.

        (2)   That, for the purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

        (3)   To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

        The undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act of 1933, each filing of the registrant's annual report pursuant to Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

        Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling person of the registrant pursuant to the General Corporation Law of the State of Delaware, the certificate of incorporation or the by-laws of registrant, indemnification agreements entered into between registrant and its directors, or otherwise, the registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the

II-3

question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.

        The undersigned registrant hereby undertakes that:

        (1)   For purposes of determining liability under the Securities Act of 1933, the information omitted from the form of prospectus filed as part of this registration statement in reliance upon Rule 430A and contained in a form of prospectus filed by the registrant pursuant to Rule 424(b)(1) or (4) or 497(h) under the Securities Act shall be deemed to be part of this registration statement as of the time it was declared effective.

        (2)   For the purpose of determining any liability under the Securities Act of 1933, each post-effective amendment that contains a form of prospectus shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

II-4

SIGNATURES

        Pursuant to the requirements of the Securities Act of 1933, as amended, the registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this registration statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the city of Cambridge, the Commonwealth of Massachusetts, on this 12^th day of October, 2004.

ADVANCED MAGNETICS, INC.
By:	/s/  JEROME GOLDSTEIN Jerome Goldstein Chairman of the Board, Chief Executive Officer, President and Treasurer

POWER OF ATTORNEY

        We, the undersigned officers and directors of Advanced Magnetics, Inc. hereby severally constitute Jerome Goldstein and Michael N. Avallone and each of them singly, our true and lawful attorneys with full power to them, and each of them singly, to sign for us and in our names in the capacities indicated below, any and all amendments (including post-effective amendments) to this registration statement on Form S-3, and to file the same with the Securities and Exchange Commission, and generally to do all such things in our names and on our behalf in our capacities as officers and directors to enable Advanced Magnetics, Inc. to comply with the provisions of the Securities Act, and all requirements of the Securities and Exchange Commission, hereby ratifying and confirming our signatures as they may be signed by our said attorneys, or any of them, to said registration statement and any and all amendments thereto.

        Pursuant to the requirements of the Securities Act of 1933, as amended, this registration statement on Form S-3 has been signed by the following persons in the capacities and on the dates indicated.

SIGNATURE	TITLE	DATE
/s/  JEROME GOLDSTEIN Jerome Goldstein	Chairman of the Board, Chief Executive Officer, President and Treasurer (principal executive and financial officer)	October 12, 2004
/s/  MICHAEL N. AVALLONE Michael N. Avallone	Chief Financial Officer, Vice President of Finance (principal accounting officer)	October 12, 2004
/s/  SHELDON L. BLOCH Sheldon L. Bloch	Director	October 12, 2004
/s/  MICHAEL D. LOBERG Michael D. Loberg	Director	October 12, 2004

II-5

/s/  BRIAN J.G. PEREIRA Brian J.G. Pereira	Director	October 12, 2004
/s/  EDWARD B. ROBERTS Edward B. Roberts	Director	October 12, 2004
/s/  MARK SKALETSKY Mark Skaletsky	Director	October 12, 2004
/s/  THEODORE I. STEINMAN Theodore I. Steinman	Director	October 12, 2004

II-6

QuickLinks

TABLE OF CONTENTS
ABOUT THIS PROSPECTUS
CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS
OUR COMPANY
RISK FACTORS
RATIO OF EARNINGS TO COMBINED FIXED CHARGES AND PREFERENCE STOCK DIVIDENDS
USE OF PROCEEDS
DESCRIPTION OF OUR COMMON STOCK
DESCRIPTION OF OUR PREFERRED STOCK
DESCRIPTION OF OUR WARRANTS
DESCRIPTION OF CERTAIN PROVISIONS OF DELAWARE LAW AND OUR CERTIFICATE OF INCORPORATION AND BY-LAWS
PLAN OF DISTRIBUTION
VALIDITY OF THE OFFERED SECURITIES
EXPERTS
DOCUMENTS INCORPORATED BY REFERENCE
WHERE YOU CAN FIND MORE INFORMATION
PART II INFORMATION NOT REQUIRED IN PROSPECTUS

Item 14. Other Expenses of Issuance and Distribution.
Item 15. Indemnification of Directors and Officers.
Item 16. Exhibits.
Item 17. Undertakings.

SIGNATURES

EX-5.1

QuickLinks -- Click here to rapidly navigate through this document

Exhibit 5.1

Sullivan &	Sullivan & Worcester LLP	T 617 338 2800
Worcester letterhead	One Post Office Square	F 617 338 2880
	Boston, MA 02109	www.sandw.com

October 12, 2004

Advanced Magnetics, Inc.
61 Mooney Street
Cambridge, MA 02138

Re:

Advanced Magnetics, Inc. Registration Statement on Form S-3

Ladies and Gentlemen:

        We are rendering this opinion in connection with a registration statement on Form S-3 (the "Registration Statement") to be filed on or about the date hereof by Advanced Magnetics, Inc., a Delaware corporation (the "Company"), with the Securities and Exchange Commission (the "Commission") under the Securities Act of 1933, as amended (the "Securities Act"). The Registration Statement relates to the proposed issuance and sale from time to time, pursuant to Rule 415 under the Securities Act as set forth in the final prospectus that forms a part of the Registration Statement (the "Prospectus") and as to be set forth in one or more final supplements to the Prospectus (each, a "Prospectus Supplement"), of up to $50,000,000 in aggregate amount of the following securities (the "Registered Securities"): (i) shares of preferred stock, $0.01 par value per share, of the Company (the "Preferred Shares"); (ii) shares of common stock, $0.01 par value per share, of the Company (the "Common Shares"); and (iii) warrants to purchase Preferred Shares or Common Shares (the "Warrants"). The following opinion is furnished to the Company to be filed with the Commission as Exhibit 5.1 to the Registration Statement. As used in this opinion, the term "Registration Statement" includes, unless otherwise stated, such Registration Statement, as amended when declared effective by the Commission (including any necessary post-effective amendments thereto); the term "Convertible Registered Securities" means Registered Securities which are convertible into, exchangeable for or exercisable for other Registered Securities; and the term "Underlying Registered Securities" means any Registered Securities which are issuable upon conversion, exchange or exercise of Convertible Registered Securities.

        In connection with this opinion, we have examined and relied upon a copy of the Registration Statement to be filed with the Commission on or about the date hereof. We have also examined and relied upon originals or copies of such records, agreements and instruments of the Company, certificates of public officials and of officers of the Company and such other documents and records, and such matters of law, as we have deemed necessary as a basis for the opinions hereinafter expressed. In making such examination, we have assumed the genuineness of all signatures, the legal capacity of natural persons, the authenticity of all documents submitted to us as originals and the conformity to the originals of all documents submitted to us as copies, which facts we have not independently verified.

        We have necessarily assumed in connection with the opinions expressed below that the terms and conditions of the Registered Securities and any related agreements and instruments, except to the extent described in the Registration Statement and the form of preliminary prospectus contained therein, as originally filed, will be, and that any related proceedings of the Company conducted after the date hereof will be conducted, (i) in accordance with all applicable laws and the Company's Certificate of Incorporation, as amended (the "Certificate of Incorporation") and Amended and Restated By-laws and (ii) not in conflict with any contractual or other restrictions which are binding on the Company, and that, without limiting the generality of the foregoing, any agreements or instruments that are hereafter required to be filed as an exhibit to the Registration Statement will be properly filed by an amendment thereto or by the filing of a Form 8-K by the Company under the Securities

Exchange Act of 1934, as amended, and properly incorporated by reference in the Registration Statement, as permitted by the Securities Act and the rules and regulations of the Commission thereunder.

        We have also necessarily assumed in connection with the opinions expressed below that (i) the Registration Statement, and any amendments thereto (including post-effective amendments), will have become effective under the Securities Act; (ii) a Prospectus Supplement will have been filed with the Commission pursuant to Rule 424 under the Securities Act describing the Registered Securities offered thereby; (iii) the Company's Board of Directors (the "Board") or a duly authorized Committee thereof shall have duly adopted final resolutions (the "Final Resolutions") authorizing the issuance and sale of the applicable Registered Security as contemplated by the Registration Statement, the Prospectus, the applicable Prospectus Supplement and any applicable Warrant Agreement (as defined below); (iv) evidence of each Registered Security shall have been duly executed, countersigned, authenticated and registered, as required by the Warrant Agreement, if applicable, and Certificate of Incorporation, Amended and Restated By-laws and Final Resolution for that Registered Security, and shall have been duly delivered to the purchasers thereof against payment of the agreed consideration therefor (which shall, in any event, be an amount at least equal to the par value, if any, thereof), as provided in the Registration Statement, the Prospectus and the applicable Prospectus Supplement, Warrant Agreement and Final Resolutions for such Registered Security; (v) all Registered Securities will be issued and sold in compliance with applicable federal and state securities laws and in the manner stated in the Registration Statement and the applicable Prospectus Supplement; (vi) any Underlying Registered Securities being offered will be duly authorized, created and, if appropriate, reserved for issuance upon such conversion, exchange, redemption or exercise; and (vii) with respect to any Common Shares or Preferred Shares offered, or any Convertible Registered Securities as to which Common Shares or Preferred Shares are the related Underlying Registered Securities that, at the time of the issuance thereof, the Company will have a sufficient number of shares of authorized Common Shares or Preferred Shares, as the case may be, under the Certificate of Incorporation that will be unissued and not otherwise reserved for issuance.

        To the extent that the obligations of the Company under each Warrant Agreement may be dependent upon such matters, we have assumed for purposes of this opinion that (i) each Warrant Agent (as defined below) is duly organized, validly existing and in good standing under the laws of its jurisdiction of organization, and is duly qualified to engage in the activities contemplated by, and has the requisite organizational and legal power and authority to perform its obligations under, each Warrant Agreement to which it is a party; (ii) each Warrant Agent will be in compliance with all applicable laws and regulations, with respect to acting as an agent under each applicable Warrant Agreement; and (iii) each Warrant Agreement will be the valid and binding agreement of each party thereto (other than the Company), enforceable against such party in accordance with its terms.

        We express no opinion herein concerning any law other than the Delaware General Corporation Law (including the statutory provisions, all applicable provisions of the Delaware Constitution and reported judicial decisions interpreting the foregoing) and the federal laws of the United States of America, and we express no opinion as to state securities or blue sky laws.

        Our opinions set forth below with respect to the validity or binding effect of any security or obligation are subject to (i) limitations arising under applicable bankruptcy, insolvency, reorganization, fraudulent conveyance, moratorium or other similar laws affecting the enforcement generally of the rights and remedies of creditors and secured parties or the obligations of debtors; (ii) general principles of equity (regardless of whether considered in a proceeding at law or in equity), including, without limitation, the discretion of any court of competent jurisdiction in granting specific performance or injunctive or other equitable relief; and (iii) an implied duty on the part of the party seeking to enforce rights or remedies to take action and make determinations on a reasonable basis and in good faith to the extent required by applicable law.

2

        Based on and subject to the foregoing, and subject to the assumptions, limitations and qualifications set forth herein, we are of the opinion that, as of the date hereof:

        1.     Each series of Preferred Shares will be validly issued, fully paid and non-assessable by the Company when (i) the Board or a duly authorized committee thereof shall have duly adopted resolutions approving a certificate of designation setting forth the terms of such series of Preferred Shares, including establishing a sufficient quantity thereof and setting forth the preferences, restrictions, limitations as to dividends, qualifications and terms and conditions of redemption, consistent with the Final Resolutions for such series of Preferred Shares; and (ii) the certificate of designation shall have been duly executed and filed with and accepted for record by the Secretary of State of the State of Delaware. If such Preferred Shares are Underlying Registered Securities, the opinion set forth in this paragraph is subject to the further condition that the Convertible Registered Securities relating to such Preferred Shares, at the time of the issuance or delivery thereof, as applicable, and of the conversion, exchange or exercise thereof, are validly issued, fully paid and non-assessable by the Company or are valid and binding obligations of the Company, as applicable.

        2.     The Common Shares will be validly issued, fully paid and non-assessable by the Company. If such Common Shares are Underlying Registered Securities, the opinion set forth in this paragraph is subject to the condition that the Convertible Registered Securities relating to such Common Shares, at the time of the issuance or delivery thereof, as applicable, and of the conversion, exchange or exercise thereof, are validly issued, fully paid and non-assessable by the Company or are valid and binding obligations of the Company, as applicable.

        3.     The Warrants will be duly authorized and validly issued and binding obligations of the Company when (i) the Board or a duly authorized committee thereof shall have duly adopted resolutions approving one or more warrant agreements, including a form of warrant set forth therein or related thereto (each, a "Warrant Agreement"), establishing the terms and conditions of such Warrants, between the Company and a financial institution identified therein as warrant agent (each, a "Warrant Agent"); and (ii) the applicable Warrant Agreement shall have been duly executed and delivered by the Company and the Warrant Agent. If such Warrants are Underlying Registered Securities, the opinion set forth in this paragraph is subject to the further condition that the Convertible Registered Securities relating to such Warrants, at the time of the issuance or delivery thereof, as applicable, and of the conversion, exchange or exercise thereof, are validly issued, fully paid and non-assessable by the Company or are valid and binding obligations of the Company, as applicable.

        All of the opinions set forth herein are rendered as of the date hereof, and we assume no obligation to update such opinions to reflect any facts or circumstances which may hereafter come to our attention or any changes in the law which may hereafter occur.

        We hereby consent to the filing of this opinion as an exhibit to the Registration Statement and to the reference to our firm in the Prospectus forming a part of the Registration Statement. In giving such consent, we do not thereby admit that we come within the category of persons whose consent is required under Section 7 of the Securities Act or under the rules and regulations of the Commission promulgated thereunder.

Very truly yours,

/s/ Sullivan & Worcester LLP

SULLIVAN & WORCESTER LLP

3

QuickLinks

Exhibit 5.1

EX-10.1

QuickLinks -- Click here to rapidly navigate through this document

Exhibit 10.1

INDEMNIFICATION AGREEMENT

        This Indemnification Agreement (the "Agreement") dated as of August 9, 2004, by and between Advanced Magnetics, Inc., a Delaware Corporation (the "Company"); and Sheldon L. Bloch, a director and/or officer of the Company (the "Indemnitee"):

WITNESSETH:

        WHEREAS, the Indemnitee is presently serving as a director and/or officer of the Company, and the Company desires the Indemnitee to continue in such capacity;

        WHEREAS, the Company and the Indemnitee recognize the substantial increase in corporate litigation in general as well as the adoption of recently implemented corporate governance legislation, subjecting officers and directors to expensive litigation risks, including, in certain circumstances, expenses of defending a claim regardless of its merit;

        WHEREAS, the Company desires to attract and retain the services of highly qualified individuals, such as the Indemnitee, to serve as officers and directors of the Company and to indemnify its officers and directors so as to provide them with the maximum protection permitted by law;

        WHEREAS, in view of these considerations, the Company desires to provide, independent from the indemnification to which the Indemnitee is otherwise entitled by law and under the Company's certificate of incorporation and by-laws (the "Charter Documents"), indemnification to the Indemnitee and advances of expenses, all as set forth in this Agreement to the maximum extent permitted by law;

        NOW, THEREFORE, to induce the Indemnitee to continue to serve in the Indemnitee's present capacity, to provide greater certainty as to the Indemnitee's rights and obligations, and in consideration of the premises and the mutual agreements set forth in this Agreement, the Company and the Indemnitee agree as follows:

1.     Continued Service.    The Indemnitee agrees to continue to serve as a director and/or officer of the Company at the Company's will (or under separate agreement, if such agreement exists), in the capacity that the Indemnitee currently serves, for so long as the Indemnitee is duly elected or appointed and qualified in accordance with the Charter Documents or until the Indemnitee resigns in writing in accordance with applicable law or the Indemnitee's employment agreement with the Company, if the same exists, expires without extension or renewal or is terminated; provided, however, that this Agreement shall not create any obligation on the part of the Company to retain the Indemnitee in any such position or at any particular compensation.

2.     Initial Indemnity.

        (a)    Third Party Proceedings.    The Company shall indemnify the Indemnitee, to the fullest extent permitted by law, if the Indemnitee is a party or is threatened to be made a party to or is otherwise involved in (including, without limitation, as a witness) any threatened, pending or completed action, suit, arbitration, or other alternate dispute resolution mechanism, or investigation, inquiry, administrative hearing or any other actual, threatened or completed proceeding, whether civil, administrative, investigative or criminal including, without limitation, any appeal therefrom (collectively, "Proceeding") (other than an action by or in the right of the Company), by reason of (or arising in part out of) any event or occurrence related to the fact that the Indemnitee is or was or had agreed to become a director, officer, employee and/or agent of the Company, or is or was serving or had agreed to serve at the request of the Company as a director, officer, employee or agent of another corporation, partnership, joint venture, trust or other enterprise (collectively, "Corporate Status"), or by reason of any action alleged to have been taken or omitted in such capacity, against all Expenses (as defined below), judgments, fines, penalties and amounts paid in settlement (whether with or without court approval), including without limitation all interest, assessments and other charges paid or payable in connection with or in respect of the foregoing, actually and reasonably incurred by the Indemnitee

or on the Indemnitee's behalf in connection with such Proceeding or any claim, issue or matter therein, provided the Indemnitee acted in good faith and in a manner the Indemnitee reasonably believed to be in or not opposed to the best interests of the Company, and, with respect to any criminal action or proceeding, had no reasonable cause to believe the Indemnitee's conduct was unlawful. The termination of any Proceeding by judgment, order, settlement (whether with or without court approval), conviction, or upon a plea of nolo contendre or its equivalent shall not, of itself, create a presumption that the Indemnitee did not satisfy the foregoing standard of conduct to the extent applicable thereto. As used herein, "Expenses" shall mean all reasonable attorneys' fees, retainers, court costs, transcript costs, fees of experts, witness fees, travel expenses, duplicating costs, printing and binding costs, telephone charges, postage, delivery service fees, and all other disbursements or expenses of the types customarily incurred in connection with prosecuting, defending, preparing to prosecute or defend, investigating, being or preparing to be a witness in, or otherwise participating in a Proceeding, and any federal, state, local or foreign taxes imposed on the Indemnitee as a result of the actual or deemed receipt of any payments under this Agreement.

        (b)    Proceedings by or in the Right of the Company.    The Company shall indemnify the Indemnitee, to the fullest extent permitted by law if, by reason of the Indemnitee's Corporate Status, or by reason of any action alleged to have been taken or omitted on the part of the Indemnitee while serving in such capacity, the Indemnitee was or is a party or is threatened to be made a party to any threatened, pending or completed Proceeding brought in the name or right of the Company to procure a judgment in its favor against all Expenses, and to the fullest extent permitted by law, amounts paid in settlement, including without limitation all interest, assessments and other charges paid or payable in connection with or in respect of the foregoing, actually and reasonably incurred by the Indemnitee in connection with such Proceeding or any claim, issue or matter therein, provided the Indemnitee acted in good faith and in a manner the Indemnitee reasonably believed to be in or not opposed to the best interests of the Company, except that no indemnification shall be made in respect of (i) any Proceeding, claim, issue or matter as to which the Indemnitee shall have been finally adjudicated by court order or judgment to be liable to the Company, unless and only to the extent that the Delaware Court of Chancery or any other court in which such Proceeding was brought shall determine upon application that, despite the adjudication of liability but in view of all the circumstances of the case, the Indemnitee is fairly and reasonably entitled to indemnity for such reasonable Expenses which the Court of Chancery or such other court shall deem proper; and (ii) any Proceeding, claim, issue or matter in respect of which such indemnification is expressly prohibited by applicable law.

        (c)    Mandatory Payment of Expenses.    Notwithstanding any other provision of this Agreement, to the extent that the Indemnitee has been successful on the merits or otherwise, in defense of any Proceeding referred to in Sections 2(a) or 2(b) hereof or in defense of any claim, issue or matter therein, the Indemnitee shall be indemnified against all Expenses actually and reasonably incurred by the Indemnitee in connection therewith. For purposes of this Section 2 and without limitation, the termination of any claim, issue or matter in such a Proceeding by dismissal, with or without prejudice, shall be deemed to be a successful result as to such claim, issue or matter. If the Indemnitee is not wholly successful in defense of such Proceeding but is successful, on the merits or otherwise, as to one or more but less than all claims, issues or matters in such Proceeding, the Company shall indemnify the Indemnitee against all Expenses actually and reasonably incurred by the Indemnitee or on the Indemnitee's behalf in connection with each successfully resolved claim, issue or matter.

        (d)    Determination of Indemnification.    Any indemnification under Sections 2(a) or 2(b) hereof (unless ordered by a court) shall be made by the Company upon a determination in accordance with Section 3 hereof or any applicable provision of the Charter Documents, other agreement, resolution or otherwise. Such determination shall be made (i) by the Board of Directors of the Company (the "Board") by a majority vote of a quorum consisting of directors who were not parties to such Proceeding, (ii) if such a quorum of disinterested directors is not available or so directs, by

2

independent legal counsel (designated in the manner provided below in this subsection (d)) or (iii) by the stockholders of the Company (the "Stockholders"). Independent legal counsel shall be designated by vote of a majority of the disinterested directors; provided, however, that if the Board is unable or fails to so designate, such designation shall be made by the Indemnitee subject to the approval of the Company (which approval shall not be unreasonably withheld). The Company agrees to pay the reasonable fees and expenses of such independent legal counsel and to indemnify fully such counsel against costs, charges and expenses (including attorneys' and others' fees and expenses) actually and reasonably incurred by such counsel in connection with this Agreement or the opinion of such counsel pursuant hereto.

        (e)    Advancement of Expenses.    All Expenses incurred by the Indemnitee in the Indemnitee's capacity as a director or officer of the Company in connection with any Proceeding referenced in Section 2(a) or 2(b) hereof (including, without limitation, retainers and prepaid, deposited or escrowed amounts), shall be paid by the Company, as incurred, in advance of the final disposition of such Proceeding in the manner prescribed by Section 3(b) hereof.

        (f)    Company Amendments.    The Company shall not adopt any amendment to the Certificate or By-Laws, the effect of which would be to deny, diminish or encumber the Indemnitee's rights to indemnity pursuant to this Agreement, the Charter Documents, the General Corporation Law of the State of Delaware (the "GCL") or any other applicable law as applied to any act or failure to act occurring in whole or in part prior to the date (the "Effective Date") upon which the amendment was approved by the Board or the Stockholders, as the case may be. In the event that the Company shall adopt any amendment to the Certificate or By-Laws, the effect of which is to so deny, diminish or encumber the Indemnitee's rights to indemnity, such amendment shall apply only to acts or failures to act occurring entirely after the Effective Date thereof unless the Indemnitee shall have voted in favor of such adoption as a director or holder of record of the Company's voting stock, as the case may be.

        (g)    Security.    To the extent requested by the Indemnitee and approved by the Board, the Company may at any time and from time to time provide security to the Indemnitee for the Company's obligations hereunder through an irrevocable bank letter of credit, funded trust or other collateral. Any such security, once provided to the Indemnitee, may not be revoked or released without the prior written consent of the Indemnitee.

3.     Certain Procedures Relating to Indemnification and Advancement of Expenses.

        (a)    Notice.    Except as otherwise permitted or required by the GCL, for purposes of pursuing rights to indemnification under Sections 2(a) or 2(b) hereof, as the case may be, the Indemnitee may, but shall not be required to, (i) submit to the Board a statement of request for indemnification substantially in the form of Exhibit 1 attached hereto and made a part hereof (the "Indemnification Statement") stating that the Indemnitee is entitled to indemnification hereunder; and (ii) present to the Company reasonable evidence of all expenses for which payment is requested. Submission of an Indemnification Statement to the Board shall create a presumption that the Indemnitee is entitled to indemnification under Sections 2(a) or 2(b) hereof, as the case may be, and the Board shall be deemed to have determined that the Indemnitee is entitled to such indemnification unless within 30 calendar days after submission of the Indemnification Statement the Board shall determine by vote of a majority of the directors at a meeting at which a quorum is present, based upon clear and convincing evidence (sufficient to rebut the foregoing presumption), and the Indemnitee shall have received notice within such period in writing of such determination, that the Indemnitee is not so entitled to indemnification, which notice shall disclose with particularity the evidence in support of the Board's determination. The foregoing notice shall be sworn to by all persons who participated in the determination and voted to deny indemnification. The provisions of Section 2(d) and this Section 3(a) are intended to be procedural only and shall not affect the right of the Indemnitee to indemnification under this Agreement; and any determination by the Board that the Indemnitee is not entitled to indemnification

3

and any failure to make the payments requested in the Indemnification Statement shall be subject to judicial review as provided in Section 6 hereof.

        (b)   For purposes of receiving advancement of expenses pursuant to Section 2(e) hereof, the Indemnitee shall submit to the Board a statement of request for advancement of expenses substantially in the form of Exhibit 2 attached hereto and made a part hereof (the "Undertaking"), stating that (i) the Indemnitee has reasonably incurred or will reasonably incur actual expenses in defending a Proceeding and (ii) the Indemnitee undertakes to repay such amount if it shall ultimately be determined that the Indemnitee is not entitled to be indemnified by the Company under this Agreement or otherwise. Such payments shall be made by the Company within 10 days of receipt by it of such Undertaking. No security shall be required in connection with any Undertaking and any Undertaking shall be accepted without reference to the Indemnitee's ability to make repayment.

        (c)    Assumption of Defense and Selection of Counsel.    With respect to any Proceeding of which the Company is notified under Section 3(a), the Company shall be entitled to participate therein at its own expense and/or to assume the defense thereof at its own expense, with legal counsel approved by the Indemnitee, which approval shall not be unreasonably withheld, upon the delivery to the Indemnitee of written notice of its election to do so, in which case the Indemnitee shall provide the Company such information and cooperation as the Company may reasonably require in connection with such defense and as shall be within the Indemnitee's power to so provide. After delivery of such notice from the Company to the Indemnitee of its intention to assume the defense of the Proceeding, the Indemnitee's approval of Company counsel, and the retention of such counsel by the Company, the Company will not be liable to the Indemnitee under this Agreement for any fees and expenses of counsel subsequently incurred by the Indemnitee with respect to such Proceeding, other than as provided below. The Indemnitee shall have the right to retain the Indemnitee's own counsel in connection with such Proceeding, but the fees and expenses of such counsel incurred after such notice, approval and retention shall be at the expense of the Indemnitee, unless (i) the retention of counsel by the Indemnitee has been authorized by the Company, (ii) counsel to the Indemnitee shall have reasonably concluded that there may be a conflict of interest or position on any significant issue between the Company and the Indemnitee in the conduct of the defense of such action or (iii) the Company shall not in fact have retained counsel to assume the defense of such action, in each of which cases the fees and expenses of counsel for the Indemnitee shall be at the expense of the Company, except as otherwise expressly provided by this Agreement. The Company shall not be entitled, without the consent of the Indemnitee, to assume the defense of any claim brought by or in the right of the Company or as to which counsel for the Indemnitee shall have reasonably made the conclusion provided for in clause (ii) hereof. Notwithstanding the foregoing, the Company shall not be permitted to settle any Proceeding, or any claim, issue or matter therein, on behalf of the Indemnitee, without the prior written consent of the Indemnitee, unless the Company assumes full and sole responsibility for such settlement and such settlement grants the Indemnitee a complete and unqualified release in respect of any potential or resulting liability or the Indemnitee is otherwise fully indemnified against all such liability.

        (d)    Notice to Insurers.    If, at the time of the receipt by the Company of a notice of a Proceeding pursuant to Section 3(a) hereof, the Company has director and officer liability insurance in effect, the Company shall give prompt notice of the commencement, or the threat of the commencement, of such Proceeding to the insurers in accordance with the procedures set forth in the respective applicable insurance policies. The Company shall thereafter take all necessary action to cause such insurers to pay, on behalf of the Indemnitee, all amounts payable as a result of such Proceeding in accordance with the terms of such policies; provided that no such payments by such insurers shall relieve the Company of any liability or obligation which it may have to the Indemnitee except as and to the extent expressly provided under this Agreement.

4

4.     Subrogation; Duplication of Payments.

        (a)   In the event of payment under this Agreement, the Company shall be subrogated to the extent of such payment to all of the rights of recovery of the Indemnitee, who shall execute all documents required and shall do everything that may be necessary to secure such rights, including the execution of such documents necessary to enable the Company effectively to bring suit to enforce such rights.

        (b)   The Company shall not be liable under this Agreement to make any payment in connection with any claim made against the Indemnitee to the extent the Indemnitee has actually received payment (under any insurance policy, the Charter Documents or otherwise) of the amounts otherwise payable hereunder.

5.     The Indemnitee's Right to Enforce Indemnification Provisions; Presumptions and Burden of Proof; Expenses of Enforcement.

        (a)    Enforcement.    If a claim for indemnification or advancement of Expenses made to the Company pursuant to Section 3 hereof is not paid in full by the Company within 30 calendar days after a written claim has been received by the Company, the Indemnitee may at any time thereafter bring suit against the Company to recover the unpaid amount of the claim.

        (b)    No Presumptions; Burden of Proof.    In any action brought under Section 4(a) hereof, it shall be a defense to a claim for indemnification pursuant to Sections 2(a) or 2(b) hereof (other than an action brought to enforce a claim for Expenses incurred in defending any Proceeding in advance of its final disposition where the Undertaking, if any is required, has been tendered to the Company) that the Indemnitee has not met the standards of conduct which make it permissible under the GCL for the Company to indemnify the Indemnitee for the amount claimed, but the burden or proving such defense shall be on the Company. The failure of the Company (including the Board, independent legal counsel or the Stockholders) to have made a determination prior to commencement of such action that indemnification of the Indemnitee is proper in the circumstances because the Indemnitee has met the applicable standard of conduct set forth in the GCL shall not be a defense to such Indemnitee's claim or create a presumption that the Indemnitee has not met the applicable standard of conduct. In the event that a determination shall have been made pursuant to Section 2(d) of this Agreement that the Indemnitee is not entitled to indemnification, any judicial proceeding commenced pursuant to this Section 5 shall be conducted in all respects as a de novo trial, on the merits, and the Indemnitee shall not be prejudiced by reason of that adverse determination. In connection with any determination by the Company (including the Board, independent legal counsel or the Stockholders) or otherwise as to whether the Indemnitee is entitled to indemnification or Expense advances hereunder, the burden of proof shall be on the Company to establish that the Indemnitee is not so entitled, by clear and convincing evidence. For purposes of any determination of good faith, the Indemnitee shall be deemed to have acted in good faith if the Indemnitee's action is based on the records or books of account of the Company, including financial statements, or on information supplied to the Indemnitee by the officers of the Company in the course of their duties, or on the advice of legal counsel for the Company, by an independent certified public accountant or by an appraiser or other expert selected with reasonable care by the Company. The knowledge and/or actions, or failure to act, of any other director, officer, agent or employee of the Company shall not be imputed to the Indemnitee for purposes of determining the right to indemnification under this Agreement. The provisions of this Section 5(b) shall not be deemed to be exclusive or to limit in any way the other circumstances in which the Indemnitee may be deemed to have met the applicable standard of conduct set forth in this Agreement.

        (c)   It is the intent of the Company that the Indemnitee not be required to incur the expenses associated with the enforcement of the Indemnitee's rights under this Agreement by litigation or other legal action because the cost and expenses thereof would substantially detract from the benefits

5

intended to be extended to the Indemnitee hereunder. Accordingly, if it should appear to the Indemnitee that the Company has failed to comply with any of its obligations under this Agreement or in the event that the Company or any other person takes any action to declare this Agreement void or unenforceable, or institutes any action, suit or proceeding designed (or having the effect of being designed) to deny, or to recover from, the Indemnitee the benefits intended to be provided to the Indemnitee hereunder, the Company irrevocably authorizes the Indemnitee from time to time to retain counsel of the Indemnitee's choice, at the expense of the Company as hereinafter provided, to represent the Indemnitee in connection with the initiation or defense of any litigation or other legal action, whether by or against the Company or any director, officer, stockholder or other person affiliated with the Company, in any jurisdiction. Regardless of the outcome thereof, the Company shall pay and be solely responsible for any and all costs, charges and expenses (including attorneys' and others' fees and expenses) reasonably incurred by the Indemnitee (i) as a result of the Company's failure to perform this Agreement or any provision thereof or (ii) as a result of the Company or any person contesting the validity or enforceability of this Agreement or any provision thereof as aforesaid.

        (d)   The Company shall be precluded from asserting in any judicial proceeding commenced pursuant to this Section 5 that the procedures and presumptions of this Agreement are not valid, binding and enforceable and shall stipulate in any such court that the Company is bound by all the provisions of this Agreement.

6.     Additional Indemnification Rights.    Notwithstanding any other provision of this Agreement, the Company hereby agrees to indemnify the Indemnitee to the fullest extent permitted by law, notwithstanding that such indemnification is not specifically authorized by the other provisions of this Agreement, the Company's Charter Documents or by statute. In the event of any change, after the date of this Agreement, in any applicable law, statute, or rule which expands the right of a Delaware corporation to indemnify a member of its board of directors, an officer, or an agent, such changes shall be, ipso facto, within the purview of the Indemnitee's rights and the Company's obligations under this Agreement. In the event of any change in any applicable law, statute or rule which narrows the right of a Delaware corporation to indemnify a member of its board of directors or an officer, such changes, to the extent not otherwise required by such law, statute or rule to be applied to this Agreement shall have no effect on this Agreement or the parties' rights and obligations hereunder.

7.     Merger or Consolidation.    In the event that the Company shall be a constituent corporation in a consolidation, merger or other reorganization, the Company, if it shall not be the surviving, resulting or other corporation therein, shall require as a condition thereto the surviving, resulting or acquiring corporation to agree to indemnify the Indemnitee to the full extent provided in Section 2 hereof. Whether or not the Company is the resulting, surviving or acquiring corporation in any such transaction, the Indemnitee shall also stand in the same position under this Agreement with respect to the resulting, surviving or acquiring corporation as the Indemnitee would have with respect to the Company if its separate existence had continued.

8.     Nonexclusivity; Effectiveness; and Severability.

        (a)   The right to indemnification provided by this Agreement shall not be exclusive of any other rights to which the Indemnitee may be entitled under the Charter Documents, the GCL, any other statute, insurance policy, agreement, vote of stockholders or directors or otherwise, both as to actions taken or omitted in the Indemnitee's official capacity and as to actions taken or omitted in another capacity while holding such office, and shall continue after the Indemnitee has ceased to be a director, officer, employee or agent and shall inure to the benefit of the Indemnitee's heirs, executors and administrators. This Agreement shall be effective as of the date set forth on the first page and shall apply to acts or omissions of the Indemnitee that occurred prior to, on, and/or after such date, provided that the Indemnitee was serving in an indemnified capacity at the time such act or omission occurred.

6

        (b)   If any provision or provisions of this Agreement or the application of any provision hereof to any person or circumstances is held invalid, illegal or otherwise unenforceable, the validity, legality and enforceability of the remaining provisions of this Agreement and the application of such provision to other persons or circumstances (including, without limitation, each portion of any Section of this Agreement containing any such provision held to be invalid, illegal or unenforceable, that is not itself invalid, illegal or unenforceable) shall not in any way be affected or impaired thereby, and the provision or provisions so held to be invalid, illegal or otherwise unenforceable shall be deemed reformed to the extent (and only to the extent) necessary to make it valid, legal and enforceable and to give the maximum effect to the intent of the parties hereto. Without limiting the generality of the foregoing, if this Agreement or any portion hereof shall be invalidated on any ground by any court of competent jurisdiction, then the Company shall nevertheless indemnify the Indemnitee to the fullest extent permitted by any applicable portion of this Agreement that shall not have been invalidated, and the balance of this Agreement not so invalidated shall be enforceable in accordance with its terms.

9.     Partial Indemnification.    If the Indemnitee is entitled under any provision of this Agreement to indemnification by the Company for some or a portion of the Expenses, judgments, penalties, fines and amounts paid in settlement (including without limitation all interest, assessments and other charges paid or payable in connection with or in respect of such Expenses, judgments, penalties, fines and amounts paid in settlement) actually and reasonably incurred by the Indemnitee or on the Indemnitee's behalf in connection with such Proceeding or any claim, issue or matter therein, but not, however, for the total amount thereof, the Company shall nevertheless indemnify the Indemnitee for the portion to which the Indemnitee is entitled.

10.   Exceptions.    Any other provision herein to the contrary notwithstanding, the Company shall not be obligated pursuant to the terms of this Agreement:

        (a)    Claims Initiated by the Indemnitee.    To indemnify or advance Expenses to the Indemnitee with respect to any Proceedings initiated or brought voluntarily by the Indemnitee and not by way of defense, counterclaim or crossclaim, except (i) to the extent not otherwise prohibited by this Agreement, with respect to Proceedings brought to establish or enforce a right to indemnification under this Agreement or any other agreement or insurance policy or under the Charter Documents or any applicable statute or other law, (ii) in specific cases if the Board has approved the initiation or bringing of such Proceeding, or (iii) as otherwise required under Section 145 of the GCL, regardless of whether the Indemnitee ultimately is determined to be entitled to such indemnification, or insurance recovery, as the case may be; or

        (b)    Lack of Good Faith.    To indemnify the Indemnitee with respect to any Proceedings instituted by the Indemnitee to enforce or interpret this Agreement, if a court of competent jurisdiction determines that each of the material assertions made by the Indemnitee in such Proceeding was not made in good faith or was frivolous; or

        (c)    Insured Claims.    To indemnify the Indemnitee for Expenses or liabilities of any type whatsoever (including, but not limited to, judgments, fines, penalties, and amounts paid in settlement) to the extent such Expenses or liabilities have been paid directly to the Indemnitee by an insurance carrier under a policy of insurance; or

        (d)    Claims under Section 16(b).    To indemnify the Indemnitee for the payment of profits inuring to and recoverable by the Company pursuant to Section 16(b) of the Securities Exchange Act of 1934, as amended, or any similar successor statute, and any Expenses incurred with respect thereto; or

        (e)    Other Court Determinations.    To indemnify the Indemnitee for any acts or omissions, or transactions, from which a court of competent jurisdiction finally determines an officer or director, as applicable, may not be relieved of liability under applicable law or pertinent public policy; or

7

        (f)    Fraud.    To indemnify the Indemnitee if a court of competent jurisdiction finally determines that the Indemnitee has committed fraud on the Company.

11.   Mutual Acknowledgement Regarding Public Policy.    Both the Company and the Indemnitee acknowledge that in certain instances, federal law or applicable public policy may prohibit the Company from indemnifying its directors and officers under this Agreement or otherwise. The Indemnitee understands and acknowledges that the Company has undertaken or may be required in the future to undertake with the Securities and Exchange Commission (the "SEC") to submit the question of indemnification to a court in certain circumstances for a determination of the Company's right under public policy to indemnify the Indemnitee.

12.   Director and Officer Liability Insurance.    In all policies of director and officer liability insurance maintained by the Company (if any), the Indemnitee shall be named as an insured in such a manner as to provide the Indemnitee the same rights and benefits as are accorded to the most favorably insured of the Company's directors, if the Indemnitee is a director of the Company; or of the Company's officers, if the Indemnitee is not a director of the Company but is an officer thereof.

13.   Governing Law.    This Agreement and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed by, construed and interpreted in accordance with the laws of the State of Delaware, without giving effect to the principles of conflict of laws thereof.

14.   Consent to Jurisdiction.    The Company and the Indemnitee each hereby irrevocably consent to the personal jurisdiction of the Court of Chancery of Delaware for any purpose in connection with any actions or Proceedings that arise out of or relate to this Agreement.

15.   Modification; Survival.    This Agreement contains the entire agreement and understanding of the parties relating to the subject matter hereof. This Agreement may be modified or amended only by an instrument in writing signed by both parties hereto. No amendment, alteration or repeal of this Agreement or of any provision hereof shall limit or restrict any right of the Indemnitee under this Agreement in respect of any action taken or omitted by the Indemnitee in the Indemnitee's Corporate Status prior to such amendment, alteration or repeal. The failure by either party to enforce any rights under this Agreement shall not be construed as a waiver of any rights of such party. This Agreement shall survive the death, disability, or incapacity of the Indemnitee or the termination of the Indemnitee's service as a director and officer of the Company and shall inure to the benefit of the Indemnitee's heirs, executors and administrators.

16.   Notices.    All notices, request, demands and other communications hereunder shall be in writing and shall be deemed to have been duly given (i) upon delivery, if delivered by hand and receipted for by the party to whom said notice or other communication shall have been directed, (ii) on the first business day after the date on which it is mailed by overnight courier service or transmitted via facsimile or (iii) on the third business day after the date on which it is mailed by certified or registered mail with postage prepaid:

(i)

If to the Indemnitee, at the address specified on the signature page of this Agreement; and



(ii)

If to the Company to:


Advanced Magnetics, Inc.
61 Mooney Street
Cambridge, MA 02138

or to such other address as may have been furnished in writing pursuant to this Section 16 to the Indemnitee by the Company or to the Company by the Indemnitee, as the case may be.

8

17.   Counterparts.    This Agreement may be executed in two or more counterparts, each of which shall be deemed an original and all of which together shall constitute one instrument.

18.   Company Acknowledgement Regarding Consideration.    The Company expressly confirms and agrees that it has entered into this Agreement and assumed the obligations imposed on it hereby in order to induce the Indemnitee to serve as a director, officer, employee and/or agent of the Company, and the Company acknowledges that the Indemnitee is relying upon this Agreement in serving in such capacity.

19.   Certain Terms.    For purposes of this Agreement, references to the "Company" shall include, in addition to Advanced Magnetics, Inc., any constituent corporation (including any constituent of a constituent) absorbed in a consolidation or merger to which Advanced Magnetics, Inc., (or any of its subsidiaries) is a party which, if its separate existence had continued, would have had power and authority to indemnify its directors, officers, and employees or agents, so that if the Indemnitee is or was a director, officer, employee or agent of such constituent corporation, or is or was serving at the request of such constituent corporation as a director, officer, employee or agent of another corporation, partnership, joint venture, trust or other enterprise, the Indemnitee shall stand in the same position under the provisions of this Agreement with respect to the resulting or surviving corporation as the Indemnitee would have with respect to such constituent corporation if its separate existence had continued; references to "other enterprises" shall include employee benefit plans; references to "fines" shall include any excise taxes assessed on the Indemnitee with respect to any employee benefit plan; and references to "serving at the request of the Company" shall include any service as a director, officer, employee or agent of the Company which imposes duties on, or involves services by, the Indemnitee with respect to an employee benefit plan, its participants or beneficiaries; references to the masculine shall include the feminine; references to the singular shall include the plural and vice versa; and if the Indemnitee acted in good faith and in a manner a reasonably believed to be in the interest of the participants and beneficiaries of an employee benefit plan, the Indemnitee shall be deemed to have acted in a manner "not opposed to the best interests of the Company" as referenced to herein.

20.   Company Compliance with Law.    Nothing in this Agreement is intended to require or shall be construed as requiring the Company to do or fail to do any act in violation of applicable law. The Company's inability, pursuant to court order, to perform its obligations under this Agreement shall not constitute a breach of this Agreement.

21.   Prior Agreement Terminated.    Indemnitee acknowledges that this Agreement supersedes in its entirety any prior Indemnification Agreement to which the Company and the Indemnitee may be parties.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

9

        IN WITNESS WHEREOF, the parties hereto have duly executed this Agreement as of the date first above written.

ADVANCED MAGNETICS, INC.
By:	/s/  JEROME GOLDSTEIN
Printed Name:	Jerome Goldstein
INDEMNITEE
By:	/s/  SHELDON L. BLOCH
Printed Name:	Sheldon L. Bloch
Address:	[address omitted]

10

Exhibit 1
INDEMNIFICATION STATEMENT

STATE OF _________________________________	)
	)	SS
COUNTY OF ______________________________	)

I, [NAME], being first duly sworn, do depose and say as follows:

        1.     This Indemnification Statement is submitted pursuant to the Indemnification Agreement dated as of                        , 2004 between ADVANCED MAGNETICS, INC., a Delaware corporation (the "Company"), and the undersigned.

        2.     I am requesting indemnification against charges, costs, expenses (including attorneys' and others' fees and expenses), judgments, fines and amounts paid in settlement, all of which (collectively, "Liabilities") have been or will be incurred by me in connection with an actual or threatened action, suit, proceeding or claim to which I am a party or am threatened to be made a party.

        3.     With respect to all matters related to any such action, suit, proceeding or claim, I am entitled to be indemnified as herein contemplated pursuant to the aforesaid Indemnification Agreement.

        4.     Without limiting any other rights which I have or may have, I am requesting indemnification against Liabilities which have or may arise out of

        5.     Attached is a copy of any and all summons, citations, subpoenas, complaints, indictments and/or other documents that I have received in connection with the aforementioned action, suit proceeding or claim.

        Subscribed and sworn to before me, a Notary Public in and for said County and State, this    day of                        , 200    .

___________________________________

[Seal]

        My commission expires the            day of                        20    .

Exhibit 2
UNDERTAKING

STATE OF _________________________________	)
	)	SS
COUNTY OF ______________________________	)

I, being first duly sworn, do depose and say as follows:

        1.     This Undertaking is submitted pursuant to the Indemnification Agreement dated as of            , 2004 between ADVANCED MAGNETICS, INC., a Delaware corporation (the "Company"), and the undersigned.

        2.     I am requesting advancement of certain costs, charges and expenses which I have incurred or will incur in defending an actual or pending civil or criminal action, suit, proceeding or claim.

        3.     I hereby undertake to repay this advancement of expenses if it shall ultimately be determined that I am not entitled to be indemnified by the Company under the aforesaid Indemnification Agreement or otherwise.

        4.     The costs, charges and expenses for which advancement is requested are, in general, all expenses related to

        Subscribed and sworn to before me, a Notary Public in and for said County and State, this            day of                        , 200            .

___________________________________

[Seal]

        My commission expires the            day of            , 20    .

Schedule to Exhibit 10.1

        The following individuals are parties to Indemnification Agreements with the Company which are substantially identical in all material respects to the representative Indemnification Agreement filed herewith and are dated as of the respective dates listed below. The other Indemnification Agreements are omitted pursuant to Instruction 2 to Item 601 of Regulation S-K.

Name of Signatory	Date
Jerome Goldstein	August 9, 2004
Sheldon L. Bloch	August 9, 2004
Michael D. Loberg	August 9, 2004
Brian J.G. Pereira	August 9, 2004
Edward B. Roberts	August 9, 2004
Mark Skaletsky	August 9, 2004
Theodore I. Steinman	August 9, 2004

QuickLinks

Exhibit 10.1

INDEMNIFICATION AGREEMENT

EX-12.1

QuickLinks -- Click here to rapidly navigate through this document

Exhibit 12.1

RATIO OF EARNINGS TO COMBINED FIXED CHARGES AND PREFERENCE DIVIDENDS

			FY 1999			FY 2000			FY 2001			FY 2002			FY 2003		YTD FY 2004 through 6/30/04
Fixed charges:
	Interest expensed and capitalized		$	—		$	—		$	—		$	—		$	—	$	—
	Amortized premiums, discounts and capitalized expenses related to indebtedness		$	—		$	—		$	—		$	—		$	—	$	—
	Estimate of interest within rental expense—from continuing operations*			86,285			67,269			52,244			35,633			4,729		3,787
	Preference security dividend requirements of consolidated subsidiaries (pre-tax earnings requirement)
		Total—combined fixed charges and preference dividends	$	86,285		$	67,269		$	52,244		$	35,633		$	4,729	$	3,787
Earnings:
	Pre-tax income from continuing operations before adjustments for minority interests in consolidated subsidiaries or income or loss from equity investments			(4,442,218	)		(3,805,768	)		(3,803,823	)		(1,706,272	)		742,105		(2,284,388	)
							NOTE 1
	Fixed Charges*			86,285			67,269			52,244			35,633			4,729		3,787
	Amortization of Capitalized Interest			—			—			—			—			—		—
	Distributed Income of equity investees			—			—			—			—			—		—
	Share of pre-tax losses of equity investees for which charges arising from guarantees are included in fixed charges			—			—			—			—			—		—
		Subtotal		(4,355,933	)		(3,738,499	)		(3,751,579	)		(1,670,639	)		746,834		(2,280,601	)
Deduct:
	Interest capitalized			—			—			—			—			—		—
	Preference security dividend requirements of consolidated subsidiaries			—			—			—			—			—		—
	Minority interest in pre-tax income of subsidiaries that have not incurred fixed charges						—			—			—			—		—
Total Earnings			$	(4,355,933	)	$	(3,738,499	)	$	(3,751,579	)	$	(1,670,639	)	$	746,834	$	(2,280,601	)
Ratio of earnings to combined fixed charges and preference dividends				(50.5	)		(55.6	)		(71.8	)		(46.9	)		157.9		(602.2	)
Deficiency			$	4,442,218		$	3,805,768		$	3,803,823		$	1,706,272			N/A	$	2,284,388

*

represents estimated interest associated with certain facility, equipment and vehicle leases (at an assumed rate of 20% of total rent expense for facility and equipment leases).

NOTE 1: FY 2000 pre-tax income excludes a $7,457,717 loss associated with a cumulative effect of an accounting change.

QuickLinks

Exhibit 12.1

EX-23.1

QuickLinks -- Click here to rapidly navigate through this document

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

        We hereby consent to the incorporation by reference in this Registration Statement on Form S-3 of our report dated November 11, 2003 relating to the financial statements which appears in Advanced Magnetics, Inc.'s Annual Report on Form 10-K for the year ended September 30, 2003. We also consent to the references to us under the heading "Experts" in such Registration Statement.

/s/ PricewaterhouseCoopers LLP
PricewaterhouseCoopers LLP

Boston, Massachusetts
October 12, 2004

QuickLinks

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM