S-3MEF

QuickLinks -- Click here to rapidly navigate through this document

As filed with the Securities and Exchange Commission on December 7, 2006

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.)
125 CambridgePark Drive, 6th Floor Cambridge, MA 02140 (617) 498-3300 (Address, including zip code, and telephone number, including area code, of registrant's principal executive offices)
Brian J. G. Pereira, MD Chief Executive Officer and President Advanced Magnetics, Inc. 125 CambridgePark Drive, 6th Floor Cambridge, MA 02140 (617) 498-3300 (Name, address, including zip code, and telephone number, including area code, of agent for service)

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

Approximate date of commencement of proposed sale to the public: As soon as practicable after this registration statement becomes effective.

        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.    o

        If this form is filed to register additional securities for an offering pursuant to Rule 462(b) 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.    ý 333-136552

        If this form is a post-effective amendment filed pursuant to Rule 462(c) 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 registration statement pursuant to General Instruction I.D. or a post-effective amendment thereto that shall become effective upon filing with the Commission pursuant to Rule 462(e) under the Securities Act, check the following box.    o

        If this form is a post-effective amendment to a registration statement filed pursuant to General Instruction I.D. filed to register additional securities or additional classes of securities pursuant to Rule 413(b) under the Securities Act, check the following box.    o

CALCULATION OF REGISTRATION FEE

Title of each class of securities to be registered	Proposed maximum aggregate offering price(1)	Amount of registration fee(2)
Common Stock ($.01 par value)
Total	$25,000,000	$2,675.00

(1)

In accordance with Rule 457(o) under the Securities Act of 1933, as amended, the number of shares being registered and the proposed maximum offering price per share are not included in this table.

(2)

The registrant certifies to the Securities and Exchange Commission (the "Commission") that it has instructed its bank to pay the Commission the filing fee set forth above for the additional shares of common stock being registered hereby by wire transfer as soon as practicable (but in any event no later than the close of business on December 8, 2006); that it will not revoke such instructions; and that it has sufficient funds in such account to cover the amount of such filing fee.

EXPLANATORY NOTE
AND INCORPORATION OF CERTAIN INFORMATION BY REFERENCE

        This Registration Statement is being filed pursuant to Rule 462(b) solely to increase the amount of shares of common stock which may be issued by us by registering an additional $25,000,000 of our common stock, $.01 par value per share. Pursuant to Rule 462(b), the contents of the Registration Statement on Form S-3 (Registration Number 333-136552), as amended, declared effective on August 23, 2006, including the exhibits thereto and each of the documents incorporated therein by reference, are hereby incorporated by reference into this Registration Statement.

2

PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

Item 16. Exhibits

5.1

Opinion of Sullivan & Worcester LLP as to the legality of the securities being registered.

23.1

Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm.

23.2

Consent of Sullivan & Worcester LLP (included in Exhibit 5.1).

24.1

Powers of Attorney (included in the signature pages of this registration statement).

3

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 7th day of December, 2006.

ADVANCED MAGNETICS, INC.
By:	/s/  BRIAN J.G. PEREIRA, MD Brian J.G. Pereira, MD Chief Executive Officer and President

POWER OF ATTORNEY

        We, the undersigned officers and directors of Advanced Magnetics, Inc. hereby severally constitute Brian J.G. Pereira and Jerome Goldstein 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	Executive Chairman and Treasurer	December 7, 2006
/s/  BRIAN J.G. PEREIRA, MD Brian J.G. Pereira, MD	Chief Executive Officer, President and Director (principal executive officer)	December 7, 2006
/s/  MICHAEL N. AVALLONE Michael N. Avallone	Chief Financial Officer and Vice President of Finance (principal financial and accounting officer)	December 7, 2006
/s/  MICHAEL D. LOBERG Michael D. Loberg	Director	December 7, 2006

4

/s/  MICHAEL NARACHI Michael Narachi	Director	December 7, 2006
/s/  MARK SKALETSKY Mark Skaletsky	Director	December 7, 2006
/s/  DAVID S. SCOON David S. Scoon	Director	December 7, 2006
/s/  RON ZWANZINGER Ron Zwanzinger	Director	December 7, 2006

5

EXHIBIT INDEX

Exhibit No.	Description of Documents
5.1	Opinion of Sullivan & Worcester LLP as to the legality of the securities being registered.
23.1	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm.
23.2	Consent of Sullivan & Worcester LLP (included in Exhibit 5.1).
24.1	Powers of Attorney (included in the signature pages of this registration statement).

6

QuickLinks

EXPLANATORY NOTE AND INCORPORATION OF CERTAIN INFORMATION BY REFERENCE
PART II INFORMATION NOT REQUIRED IN PROSPECTUS
SIGNATURES
POWER OF ATTORNEY
EXHIBIT INDEX

EX-5.1

Exhibit 5.1

[Letterhead of Sullivan & Worcester LLP]

December 7, 2006

Advanced Magnetics, Inc.
125CambridgePark Drive, 6^th Floor
Cambridge, MA 02140

Re:

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

Ladies and Gentlemen:

        We are rendering this opinion in connection with (i) a registration statement on Form S-3 Reg. No. 333-136552, as declared effective on August 23, 2006 (the "Original Registration Statement"), filed 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"), and (ii) a registration statement on Form S-3 to be filed on or about the date hereof (the "Registration Statement", and together with the Original Registration Statement, the "Registration Statements") by the Company with the Commission under the Securities Act pursuant to Rule 462(b) under the Securities Act.

        The Registration Statement relates to the proposed issuance and sale as set forth in the final prospectus (the "Prospectus") and prospectus supplement (the "Prospectus Supplement") that form a part of the Original Registration Statement and are incorporated by reference into the Registration Statement, of up to $25,000,000 in aggregate amount of shares of common stock, $.01 par value per share, of the Company (the "Common Shares").

        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 terms "Original Registration Statement" and "Registration Statement" include, unless otherwise stated, such Original Registration Statement or Registration Statement, as amended, when declared effective by the Commission (including any necessary post-effective amendments thereto).

        In connection with this opinion, we have examined and relied upon a copy of: (i) the Original Registration Statement filed with the Commission on August 11, 2006; (ii) the Registration Statement to be filed with the Commission on or about the date hereof; and (iii) the Certificate of Incorporation of the Company, as amended (the "Certificate of Incorporation"). 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 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.

        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, the Common Shares will be validly issued, fully paid and non-assessable by the Company.

        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 under the caption "Legal Matters" in the Prospectus and Prospectus Supplement incorporated by reference into 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

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 December 1, 2006 relating to the financial statements, management's assessment of the effectiveness of internal control over financial reporting and the effectiveness of internal control over financial reporting, which appears in Advanced Magnetics, Inc.'s Annual Report on Form 10-K for the year ended September 30, 2006.

/s/ PricewaterhouseCoopers LLP
Boston, MA
December 7, 2006

QuickLinks

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM