40 Manning Road
Billerica, MA 01821
(978) 663-3660
(Address, including zip code, and telephone number, including
area code, of registrant's principal executive offices)

Frank H. Laukien, Ph.D.
Chairman, President and Chief Executive Officer
40 Manning Road
Billerica, MA 01821
(978) 663-3660
(Name, address, including zip code, and telephone number, including
area code, of agent for service or process)

With a copy to:

Richard M. Stein, Esq.
Nixon Peabody LLP
100 Summer Street
Boston, Massachusetts 02110
(617) 345-1000

Approximate date of commencement of proposed sale to the public:As soon as practicable
From time to time 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 reinvestment plans, check the following box.    oý

           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 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

           Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of "large accelerated filer," "accelerated filer" and "smaller reporting company" in Rule 12b-2 of the Exchange Act.

CALCULATION OF REGISTRATION FEE

(1)

Estimated solely for purposesthe purpose of computingcalculating the registration fees pursuant tofee in accordance with Rule 457(c) under the Securities Act of 1933, as amended, based onupon the average of the high and low prices of the registrant's common stock on December 12, 2006, as reported byon the Nasdaq Global Market.Select Market on June 10, 2009.

           The Registrantregistrant hereby amends this registration statement on such date or dates as may be necessary to delay its effective timedate until the Registrantregistrant 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 or until thethis registration statement shall become effective on such date as the 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, and the selling stockholders 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 norand it is itnot soliciting offersan offer to buy these securities in any state where the offer or sale is not permitted.

PRELIMINARY PROSPECTUS (Subject to Completion)
Dated DecemberSUBJECT TO COMPLETION, DATED JUNE 15, 20062009

10,400,000 SHARESPROSPECTUS

BRUKER BIOSCIENCES CORPORATION

COMMON STOCKCommon Stock

        We may offer and sell, from time to time, up to 35,000,000 primary shares of our common stock. In addition, the selling stockholders identifiednamed under the heading "Selling Stockholders" in this prospectus may offer and sell, from time to time, up to 35,000,000 secondary shares of our common stock. We will not receive any of the proceeds from the sale of the selling stockholders' shares. Neither we nor the selling stockholders are offering 10,400,000required to sell any of these shares.

        We or the selling stockholders may offer for sale the shares of our common stock par value $.01 per share. Ofin a number of different ways and at market prices prevailing at the time of sale or at privately negotiated prices, as we more fully describe in the section entitled "Plan of Distribution" in this prospectus. When we or the selling stockholders offer shares of our common stock, offered, 2,200,000 shares are being offered by us and 8,200,000 shares are being offered bywe will provide the selling stockholders. We will not receive any proceeds from the sale of shares by anyspecific terms of the selling stockholders.offerings in supplements to this prospectus. The prospectus supplement for each offering will describe in detail the plan of distribution for that offering and will set forth the names of any underwriters, dealers or agents involved in the offering and any applicable fees, commissions, or discount arrangements. You should read this prospectus and any accompanying prospectus supplement carefully before you make your investment decision.

        Our common stock is traded on the Nasdaq Global Select Market under the symbol "BRKR." On DecemberJune 12, 2006,2009, the reported last sale price of our common stock on the Nasdaq Global Select Market was $7.98$8.36 per share.

Investing in our common stock involves risks. See "Risk Factors" beginning on page 6.1.

PRICE: $             PER SHARE

        We and the selling stockholders have granted an over-allotment option to the underwriters. Under this option, the underwriters may elect to purchase a maximum of 1,560,000 additional shares, in the aggregate, of our common stock from us and the selling stockholders, on a proportionate basis, within 30 days following the date of this prospectus to cover over-allotments, if any.

        Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacyaccuracy or accuracyadequacy of this prospectus. Any representation to the contrary is a criminal offense.

        Delivery of the shares of common stock is expected on or about                         , 2007.

The date of thisthe prospectus is                , 2007.2009.

Table of Contents

TABLE OF CONTENTS

IMPORTANT NOTICE TO READERSABOUT THIS PROSPECTUS

        This prospectus is part of a registration statement we filed with the Securities and Exchange Commission, or SEC, using the "shelf" registration process. Under the shelf registration process, using this prospectus, together with a prospectus supplement, we may, from time to time, offer and sell up to an aggregate of 35,000,000 primary shares of our common stock, in one or more offerings and at prices and on terms that we determine at the time of the offering. In addition, the selling stockholders named in this prospectus under the caption "Selling Stockholders" may offer and sell, from time to time, in one or more offerings, up to an aggregate of 35,000,000 secondary shares of our common stock.

        Each time we or the selling stockholders offer and sell shares of our common stock pursuant to this prospectus, we will provide a prospectus supplement that will contain specific information about the terms of that offering. The prospectus supplement may also add to, update or change information contained in this prospectus and, accordingly, to the extent inconsistent, the information in this prospectus is superseded by the information in the prospectus supplement. You should read this prospectus, the applicable prospectus supplement and the additional information incorporated by reference in this prospectus described below under the heading "Where You Can Find More Information" before making an investment decision. This prospectus may not be used to sell shares of our common stock unless accompanied by a prospectus supplement.

        This prospectus contains summaries of certain provisions contained in some of the documents described herein, but reference is made to the actual documents for complete information. All of the summaries are qualified in their entirety by the actual documents. Copies of the documents referred to herein have been filed, or will be filed or incorporated by reference as exhibits to the registration statement of which this prospectus is a part, and you may obtain copies of those documents as described below under the heading "Where You Can Find More Information."

        You should rely only on the information contained in or incorporated by reference in this prospectus. Neither we nor the selling stockholdersprospectus or a prospectus supplement. We have not authorized anyone to provide you with information different from the information contained in or incorporated by reference in this prospectus. If anyone provides you with different or inconsistent information, you shouldinformation. We are not rely on it. We and the selling stockholders are offeringmaking an offer to sell and seeking offers to buy, our common stock onlythese securities in jurisdictionsany jurisdiction where offers and salesthe offer or sale of these securities areis not permitted. You should not assume that information contained in this prospectus, in any supplement to this prospectus, or in any document incorporated by reference in this prospectus is accurate as of any date other than the date on the front page of the document that contains the information, regardless of when this prospectus is delivered or when any sale of our common stocksecurities occurs. Before making an investment decision, you should read this prospectus along with the information incorporated by reference in this prospectus. See "Where You Can Find More Information" for more information.Our business, financial condition and results of operations may have changed since then.

        We have not taken any action to permit a public offering of the shares of common stock outside the United States or to permit the possession or distribution of this prospectus outside the United States. Persons outside the United States who come into possession of this prospectus must inform themselves about and observe any restrictions relating to the offering of the shares of common stock and the distribution of this prospectus outside of the United States.

        In this prospectus, we use the termsThe words "Bruker, BioSciences," "we," "us" and "our" toas used in this prospectus refer only to Bruker BioSciences Corporation and its subsidiaries.consolidated subsidiaries, except where the context otherwise requires or as otherwise indicated.

i

Table of Contents

SPECIAL NOTE ABOUT FORWARD-LOOKING STATEMENTSWHERE YOU CAN FIND MORE INFORMATION

        Statements in this prospectusWe file annual, quarterly and in documents incorporated by reference in this prospectus contain various forward-lookingcurrent reports, proxy statements withinand other information with the meaning of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E ofSEC under the Securities Exchange Act of 1934, as amended, or the Exchange Act, which represent our management's beliefsAct. You may read and assumptions concerning future events. When used incopy this prospectusinformation, or obtain copies of this information by mail, at prescribed rates, from the SEC's Public Reference Room at the following location:

United States Securities and in documents incorporatedExchange Commission
100 F Street, N.E.
Room 1580
Washington, D.C. 20549

        You may obtain information on the operation of the public reference room by reference, forward-lookingcalling the SEC at 1-800-SEC-0330. The SEC also maintains a website athttp://www.sec.gov that contains reports, proxy statements include, without limitation, statements regarding financial forecasts or projections, and our expectations, beliefs, intentions or future strategies that are signified byother information about issuers, like us, who file electronically with the words "expects", "anticipates", "intends", "believes" or similar language. These forward-looking statements are subject to risks, uncertainties and assumptions that could cause our actual results and the timing of certain events to differ materially from those expressed in the forward-looking statements. It is routine for our internal projections and expectations to change as the year or each quarter in the year progress, and therefore you should clearly understand that the internal projections, beliefs and assumptions upon which we base our expectations may change prior to the end of each quarter or the year. Although these expectations may change, we may not inform you if they do.SEC.

        You should understandThe SEC allows us to "incorporate by reference" into this prospectus. This means that manywe can disclose important factors, in additioninformation to those discussedyou by referring you to another document filed separately with the SEC. Any statement contained or incorporated by reference in this prospectus could cause our resultsshall be deemed to differ materially from those expressed in the forward-looking statements. Potential factors that could affect our results include those described inbe modified or superseded for purposes of this prospectus under "Risk Factors." In light of these risks and uncertainties,to the forward-looking events discussedextent that a statement contained herein, or in any subsequently filed document which also is incorporated by reference inherein, modifies or supersedes such earlier statement. Any statement so modified or superseded shall not be deemed, except as so modified or superseded, to constitute a part of this prospectus might not occur.

CAUTIONARY NOTE REGARDING FINANCIAL INFORMATION
prospectus.

        We have incorporatedThis prospectus incorporates by reference in this prospectus two different setsthe documents listed below that we have previously filed with the SEC (excluding any portions of financial statements as of December 31, 2004 and 2005 andsuch documents that have been "furnished" but not "filed" for eachpurposes of the years inExchange Act). The SEC file number for all of the three-year period ended December 31, 2005. Each of these two sets of financial statements has a basis of presentation different than the other. We have also incorporated by reference quarterly financial statements with differing bases of presentation. These financial statements are further identified below. The different presentations, required by accounting principles generally accepted in the United States, result from our acquisition in July 2006 of Bruker Optics Inc. This acquisitiondocuments is considered, for financial reporting purposes, as a combination of companies under common control and has been accounted for in a manner similar to a pooling-of-interests.000-30833.

        We have incorporated by reference in this prospectus the financial statements and other financial information (including the financial information under the caption "Management's Discussion and Analysis of Financial Condition and Results of Operations") included in our Current Report on Form 8-K dated December 15, 2006. Those financial statements and other financial information, which supersede the corresponding information included in our

•

Our Annual Report on Form 10-K for the year ended December 31, 2005, give effect to the Bruker Optics acquisition and accordingly include the financial position and results of operations of Bruker Optics as if it had been a part of Bruker BioSciences for all periods presented. In addition, the financial statements and other financial information included in our2008, filed on March 16, 2009



•

Our Quarterly Report on Form 10-Q for the quarterly periodquarter ended SeptemberMarch 31, 2009, filed on May 11, 2009



•

Our Definitive Proxy Statement on Schedule 14A, filed on April 6, 2009



•

Our Current Reports on Form 8-K filed on January 14, 2009, March 3, 2009, March 26, 2009, April 16, 2009, April 30, 20062009, May 12, 2009 and incorporated by reference herein have been preparedJune 9, 2009, each to the extent "filed" and not "furnished" pursuant to Section 13(a) of the Exchange Act



•

The description of our common stock contained in our Registration Statement on a combined basisForm 8-A, filed on June 20, 2000, and include the financial position and results of operations of Bruker Optics as if it had been a part of Bruker BioSciences for all periods presented. We refer to these financial statements and the related financial information as the "Combined Financials."

        In accordanceany amendment or reports filed with the rules and regulationsSEC for purposes of updating such description

        All documents we file pursuant to Section 13(a), 13(c), 14 or 15(d) of the SecuritiesExchange Act after the date of this prospectus and Exchange Commission, we have alsobefore all of the securities offered by this prospectus are sold are incorporated by reference in this prospectus financial statementsfrom the date of filing of the documents, except for information "furnished" under Item 2.02 and Item 7.01 of Form 8-K or other financial information (including financial"furnished" to the SEC, which is not deemed filed and not incorporated by reference herein. Information that we file with the SEC will automatically update and may replace information underin this prospectus and information previously filed with the caption "Management's Discussion and AnalysisSEC.

        You may obtain any of Financial Condition and Results of Operations") included in our Annual Report on Form 10-K forthese incorporated documents through us, or from the yearSEC through the SEC's website at the address noted above. Documents incorporated by reference are available from us

ii

Table of Contents

ended December 31, 2005without charge, excluding any exhibits to these documents unless the exhibit is specifically incorporated by reference, by requesting them from us in writing or by telephone at the following address:

Investor Relations
Bruker Corporation
40 Manning Road
Billerica, MA 01821
(978) 663-3660

        Documents may also be available on our website in the investor relations section athttp://www.bruker.com. Information contained on our website is not a prospectus and does not constitute part of this prospectus.

SPECIAL NOTE ABOUT FORWARD-LOOKING STATEMENTS

        Certain statements made in our Quarterly Reports on Form 10-Q forthis prospectus (including documents incorporated by reference) may constitute "forward-looking statements" within the quarterly periods ended March 31, 2006 and June 30, 2006. The financial statements and other financial information in these reports do not include the financial position and resultsmeaning of operations of Bruker Optics. In addition, in accordance with the rules and regulationsSection 27A of the Securities Act and Section 21E of the Exchange Commission,Act. The words "believes," "anticipates," "plans," "expects," "seeks," "estimates," "should," "will" and similar expressions generally identify forward-looking statements. These forward-looking statements are subject to certain risks and uncertainties that could cause actual results and events to differ materially from those anticipated in the forward-looking statements.

        Potential risks and uncertainties which could adversely affect our ability to obtain these results include, without limitation, the following factors: (a) adverse changes in conditions in the global economy and volatility in the capital markets, (b) the integration of businesses we have incorporated by referenceacquired or may acquire in this prospectus financial statementsthe future, (c) changing technologies, (d) product development and other financial informationmarket acceptance of Bruker Optics includedour products, (e) the cost and pricing of our products, (f) manufacturing, (g) competition, (h) dependence on collaborative partners and key suppliers, (i) capital spending and government funding policies, (j) changes in governmental regulations, (k) intellectual property rights, (l) litigation and (m) exposure to foreign currency fluctuations.

        For a discussion of important risks of an investment in our Current Reportcommon stock, including factors that could cause actual results to differ materially from results referred to in the forward-looking statements, see "Risk Factors" beginning on Form 8-K/A dated Julypage 1 2006 and filed September 14, 2006, which financialof this prospectus. Except as required by law, we are not responsible for updating or revising any forward-looking statements, and other financial information do not include the financial position and results of operations of Bruker Optics and Bruker BioScienceswhether as if they had been a consolidated entity for all periods presented. We refer to all financial statements and other financial information described in this paragraph as the "Prior Financials."

        As a result of these different bases of presentation, the Prior Financials are not comparable to the Combined Financials. In addition, under accounting principles generally accepted in the United States, the Prior Financials can no longer be viewed as the financial statements of Bruker BioSciences, even as to periods prior to the Bruker Optics acquisition. You should not rely on the Prior Financials in assessing our financial performancenew information, future events or in making an investment decision with respect to this offering. You should instead review carefully and consider the Combined Financials in making an investment decision.

        For more information on our acquisition of Bruker Optics, see Note 3 of Notes to our Consolidated Financial Statements included in our Current Report on Form 8-K, dated December 15, 2006.otherwise.

iii

Table of Contents

PROSPECTUS SUMMARYBRUKER CORPORATION

        ThisBruker is only a summaryglobal designer and does not contain allmanufacturer of the information that you should consider before investing in our common stock. You should read the entire prospectus, including "Risk Factors" and our Combined Financial Statements and schedules and related notes included or incorporated by reference in this prospectus, before deciding to invest in our common stock.You should not rely on our Prior Financials in assessing our financial performance or in making an investment decision with respect to this offering.Unless indicated otherwise, the information included in this prospectus assumes no exercise by the underwriters of their over-allotment option to purchase additional shares of common stock.

General

        We design, manufacture, service and market analytical andproprietary life science and materials research systems and associated products and services tothat address the rapidly evolving needs of oura diverse array of customers in life science, research, pharmaceutical, biotechnology and molecular diagnostics research, as well as in materials and chemical analysis in various industries and government applications. Bruker BioSciences Corporation is the publicly traded parent company of Bruker Daltonics Inc., Bruker AXS Inc. and Bruker Optics Inc.

•

Bruker Daltonics is a leading developer and provider of innovative life-science tools based onOur core technology platforms include X-ray technologies, magnetic resonance technologies, mass spectrometry technologies, optical emission spectroscopy and infrared and Raman molecular spectroscopy technologies. We also developsmanufacture and providesdistribute a broad range of field analytical systems for chemical, biological, radiological, nuclear and nuclear ("CBRN")explosives, or CBRNE, detection.



•

We also develop and manufacture low temperature and high temperature superconductors and superconducting devices for use in advanced magnet technology, physics research and energy applications. We maintain major technical and manufacturing centers in Europe, North America and Japan and we have sales offices located throughout the world.

        Bruker was incorporated in Massachusetts as Bruker Federal Systems Corporation. In February 2000, we reincorporated in Delaware as Bruker Daltonics Inc. In July 2003, we merged with Bruker AXS Inc., and we were the surviving corporation in that merger. In connection with that merger, we changed our name to Bruker BioSciences Corporation and formed two operating subsidiaries, Bruker Daltonics and Bruker AXS. In July 2006, we acquired Bruker Optics Inc. In February 2008, we acquired the Bruker BioSpin group of companies and changed our name to Bruker Corporation. Both Bruker Corporation and Bruker BioSpin were majority owned by six affiliated shareholders prior to the February 2008 acquisition. As a result, the acquisition of Bruker BioSpin was considered a business combination of companies under common control and was accounted for at historical carrying values. The financial statements and other financial information incorporated by reference in this prospectus have been prepared on a combined basis and include the financial position and results of operations of Bruker BioSpin as if it had been a part of Bruker Corporation for all periods presented.

        Our five primary operating divisions are Bruker AXS, Bruker BioSpin, Bruker Daltonics, Bruker Optics and Bruker Advanced Supercon. Bruker AXS is a leading developerin the business of designing, manufacturing and provider of life science and advanced materials research tools fordistributing advanced X-ray, instrumentationspark-OES and spark-OES toolsAFM instrumentation used in non-destructive molecular, materials and elemental analysisanalysis. Bruker BioSpin is in academic,the business of manufacturing and distributing life science tools based on magnetic resonance technology. Bruker Daltonics is in the business of designing, manufacturing and distributing life-science mass spectrometry instruments and solutions for proteomics, metabolomics and clinical research applications. Bruker Daltonics also designs, manufactures and industrial applications.



•

distributes various analytical instruments for chemical, biological, radiological, nuclear and explosives (CBRNE) detection. Bruker Optics is a leading developerin the business of designing, manufacturing and provider ofdistributing research, analytical and process analysis instruments and solutions based on infrared and Raman molecular spectroscopy technologies.

Competitive Strengths Bruker Advanced Supercon develops and Strategy

        We believe our key competitive strengths include our:

•

broad productproduces low temperature superconductors used primarily in magnetic resonance technologies, high-energy physics and service offeringsnuclear fusion research magnet applications and high temperature superconductors for use in the markets we serve;



•

commitment to innovative, reliable and performance-leading products and solutions for our customers;



•

premier global brand;



•

extensive intellectual property portfolio; and



•

global manufacturing, distribution and logistics networks.

        Our strategy is to capitalize on our proven ability to innovate and generate rapid revenue growth, both organically and through acquisitions. We believe our commitment to be an even more significant leader within our markets, to maintain above industry-standard revenue growth and to leverage our continued research and development and distribution investments, will further enhance our operating margins and improve our earnings.

Our Businesses and Products

        We believe that our products offer the following advantages to our customers:

•

high performance and specificity;



•

integrated solutions for specific applications;



•

increased productivity;

•

high quality results; and



•

cost efficiency.

        Bruker Daltonics' mass spectrometers are sophisticated devices that measure the mass or weight of a molecule and can provide accurate information on the identity, quantity and primary structure of molecules. Our mass spectrometry-based solutions often combine advanced mass spectrometry instrumentation; automated sampling and sample preparation robots; reagent kitsenergy and other disposable products, called consumables, used in conducting tests, or assays; and powerful bioinformatics software. We offer mass spectrometry systems and integrated solutions for applications, in multiple existing and emerging life-science markets including genomics, expression proteomics, clinical proteomics, metabolic and peptide biomarker profiling, drug discovery and development, molecular diagnostics research and molecular and systems biology, as well as basic molecular medicine research. Our substantial investment in research and development allows us to design, manufacture and market a broad array of products intended to meet the rapidly growing needs of our diverse customer base. Our customers include pharmaceutical companies, biotechnology companies, proteomics companies, molecular diagnostics companies, academic institutions and government agencies. In addition, we market some of our life science systems through strategic distribution arrangements with Agilent Technologies, Sequenom and others. We are also a worldwide leader in supplying mass spectrometry-based and other systemssuperconducting devices for CBRN detection in emergency response, homeland security and defense applications.these same markets.

        Bruker AXS' X-ray systems are advanced instruments that use extremely short wavelengths of energy to determine the characteristics of matter and the three-dimensional structure of molecules. Depending on the application, our X-ray systems utilize one of three core X-ray analysis methods: single crystal diffraction, known as SCD or X-ray crystallography; polycrystalline X-ray diffraction, known as XRD or X-ray diffraction; and X-ray fluorescence, known as XRF. Using our modular platforms, we often combine each of these three technology applications with sample preparation tools, automation, consumables and data analysis software. Our products, which have particular application in structural proteomics, drug discovery, nanotechnology research and materials science fields, provide our customers with the ability to determine the three-dimensional structure of specific molecules, such as proteins, and to characterize and determine the composition of materials down to the dimensions used in nanotechnology. Our customers include biotechnology and pharmaceutical companies, nanotechnology companies, semiconductor companies, raw material manufacturers, chemical companies, academic institutions and other businesses involved in materials analysis.

        Bruker Optics manufactures and distributes research, analytical and process analysis instruments based on infrared (IR), near-infrared (NIR), Raman and time-domain magnetic resonance (TD-NMR) spectroscopy. These products are utilized in industry, government and academia for a wide range of instruments and solutions for life science, pharmaceutical analysis, food and agricultural analysis in research and development, quality control and process analysis applications. As with all spectroscopic techniques, vibrational spectroscopy can be used to identify a compound and to investigate the composition of a sample. Bruker Optics utilizes Fourier Transform (FT-IR, FT-NIR and FT-Raman) and the dispersive (Raman) measurement techniques on an extensive range of laboratory and process spectrometers. Infrared spectroscopy is a type of absorption spectroscopy that uses the infrared part of the electromagnetic spectrum. Raman spectroscopy relies on the Raman scattering of a monochromatic light that yields similar and complementary analytical information. Infrared and Raman spectroscopy are widely used in both research and industry as a simple, rapid, non-destructive and reliable technique from basic sample identification and quality control to advanced research. The Bruker Optics product line is complemented by a wide range of sampling accessories and techniques which include microanalysis, high-throughput screening and many others, to help users find the best suitable solution to analyze their samples effectively.

Corporate Information

        Our principal executive offices are located at 40 Manning Road, Billerica, MassachusettsMA 01821, and our telephone number is (978) 663-3660. Our website address iswww.bruker-biosciences.com. Information contained on our website is not a prospectus and does not constitute part of this prospectus.

Selling Stockholders

        Our five largest stockholders are Frank H. Laukien, Dirk Laukien, Isolde Laukien-Kleiner, Jörg Laukien and Marc Laukien. Dirk Laukien, Isolde Laukien-Kleiner, Jörg Laukien and Marc Laukien are the selling stockholders in this offering. Dirk Laukien is a Senior Vice President of Bruker BioSciences and the President of Bruker Optics. Jörg Laukien is a member of the Board of Directors of Bruker BioSciences. Isolde Laukien-Kleiner and Marc Laukien are not actively involved with Bruker BioSciences, and are not employees, members of management or directors of Bruker BioSciences. Frank H. Laukien, our Chairman, President and Chief Executive Officer, is not selling any shares of common stock in this offering.

        As of December 12, 2006, the four selling stockholders held, in the aggregate, 44,896,300 shares, or 43.9% of our outstanding common stock. They intend to sell 8,200,000 of those shares in this offering. Upon completion of this offering, these selling stockholders will own 35.1% of our common stock, or 34.5% if the underwriters' overallotment option is exercised in full, and our public float will increase from 37.7% to 46.8% of our outstanding common stock, or 48.2%, if the underwriters' overallotment option is exercised in full. We will not receive any proceeds from the sale of shares by the selling stockholders in this offering.

THE OFFERING

(1)

Assumes that the underwriters do not exercise their over-allotment option to purchase up to 1,560,000 additional shares in the offering, including up to 330,000 shares that the underwriters may purchase from us. If the underwriters exercise this option in full, there will be 104,875,906 shares of common stock outstanding immediately after this offering. See "Underwriting."

(2)

The number of shares of common stock to be outstanding upon completion of this offering is based on 102,345,906 shares of common stock outstanding as of December 12, 2006. This number excludes 2,860,699 shares of common stock issuable upon exercise of options outstanding at a weighted average exercise price of $6.81 per share as of December 12, 2006 and 3,582,640 additional shares of common stock available for future grant under our 2000 Stock Option Plan as of December 12, 2006.

SUMMARY CONSOLIDATED FINANCIAL DATA

        On July 1, 2006, we acquired all of the outstanding stock of Bruker Optics, a company under common control. As a result, the acquisition of Bruker Optics is considered a business combination of companies under common control, and has been accounted for in a manner similar to a pooling-of-interests. The combined statement of operations data for the years ended December 31, 2003, 2004 and 2005 have been derived from Bruker BioSciences' Current Report on Form 8-K, filed December 15, 2006 and incorporated herein by reference. The consolidated statement of operations data for the nine months ended September 30, 2006 and 2005 and the consolidated balance sheet data as of September 30, 2006 have been derived from the unaudited financial statements included in Bruker BioSciences' Quarterly Report on Form 10-Q for the nine months ended September 30, 2006. Historical results are not necessarily indicative of future results. You should read the following financial information in conjunction with our consolidated financial statements and the information under "Management's Discussion and Analysis of Financial Condition and Results of Operations" incorporated by reference from our Quarterly Report on Form 10-Q for the nine months ended September 30, 2006 and our Current Report on Form 8-K, filed December 15, 2006.

        Certain Prior Financials incorporated by reference in this prospectus are presented on a basis different from the basis on which the following Combined Financials are presented and are therefore not comparable. For more information, see "Cautionary Note Regarding Financial Information."

COMBINED FINANCIALS

(1)

As adjusted to give effect to our receipt of $16,198,000 in net proceeds from our sale of 2,200,000 shares of common stock in this offering at an assumed public offering price per share of $7.92. The net proceeds amount reflects gross proceeds less the underwriting discounts and commissions and estimated offering expenses payable by us.

RISK FACTORS

        An investment in our securities involves a high degree of risk. You should carefully consider the following risks described below, as well asand all of the other information includedset forth or incorporated by reference in this prospectus before making an investment decision. Our business, financial condition or results of operations could be materially adversely affected by any of these risks. The trading price of our common stock could decline due to any of these risks, and you may lose all or part of your investment. Please note that additional risks not presently known to us or that we currently deem immaterial

Table of Contents

may also impair our business and operations. In addition, please read "Special Note About Forward-Looking Statements" where we describe additional uncertainties associated with our business and the forward-looking statements included or incorporated by reference in this prospectus. Our actual results could differ materially from those anticipated in these forward-looking statements as a result of certain factors, including the risks faced by us described below and elsewhere included or incorporated by reference in this prospectus. Please also read "Cautionary Note Regarding

Risks Related to Our Business

A prolonged downturn in global economic conditions may materially adversely affect our business.

        Our business and results of operations are affected by international, national and regional economic conditions. Financial Information," where we describemarkets in the non-comparabilityUnited States, Europe and Asia have been experiencing extreme disruption in recent months, including, among other things, extreme volatility in security prices, severely diminished liquidity and credit availability, ratings downgrades of certain investments and declining values of others. The global economy has entered a recession. We are unable to predict the likely duration and severity of the current disruptions in financial information incorporated by referencemarkets, credit availability, and adverse economic conditions throughout the world. These economic developments affect businesses such as ours and those of our customers in this prospectus.a number of ways that could result in unfavorable consequences to us. Current economic conditions or a deepening economic downturn in the United States and elsewhere, or reductions in the level of government funding for scientific research, may cause our current or potential customers to delay or reduce purchases which could, in turn, result in reductions in sales of our products, materially and adversely affecting our results of operations and cash flows. Volatility and disruption of global financial markets could limit our customers' ability to obtain adequate financing to maintain operations and proceed with planned or new capital spending initiatives, leading to a reduction in sales volume that could materially and adversely affect our results of operations and cash flow. In addition, a decline in our customers' ability to pay as a result of the economic downturn may lead to increased difficulties in the collection of our accounts receivable, higher levels of reserves for doubtful accounts and write-offs of accounts receivable, and higher operating costs as a percentage of revenues.

If our products fail to achieve and sustain sufficient market acceptance across their broad intended range of applications, we will not generate expected revenue.

        Our business strategy depends on our ability to successfully commercialize a broad range of products based on our core technology platforms, including X-ray technologies, magnetic resonance technologies, mass spectrometry technologies, vibrational spectroscopy technologies and X-ray technologysuperconducting magnet technologies for use in a variety of life science, chemistry and materials analysis applications. Some of our products have only recently been commercially launched and have achieved only limited sales to date. The commercial success of our products depends on our obtaining continued and expanding market acceptance of our mass spectrometry, infrared and Raman measurement techniques and, our X-ray analysis toolsproducts by our diverse industrial, academic, medical research and governmental customers around the world. We may fail to achieve or sustain substantial market acceptance for our products across the full range of our intended applications or in one or more of our principal intended applications. Any such failure could decrease our sales and revenue. To succeed, we must convince substantial numbers of potential customers to invest in new systems or replace their existing techniques with X-ray, magnetic resonance, mass spectrometry and vibrational spectroscopy and X-ray techniques employing our systems. Limited funding available for capital acquisitions by our customers, as well as our customers' own internal purchasing approval policies, could hinder market acceptance of our products. Our intended customers may be reluctant to make the substantial capital investment generally needed to acquire our products or to incur the training and other costs involved with replacing their existing systems with our products. We also may not be able to convince our intended customers that our systems are an attractive and cost-effective alternative to

Table of Contents

other technologies and systems for the acquisition, analysis and management of molecular information. Because of these and other factors, our products may fail to gain or sustain market acceptance.

Our products compete in markets that are subject to rapid technological change, and most of our products are based on a range of mass spectrometry, vibrational spectroscopy and X-ray technologies one or more of whichthe technologies underlying our products could be made obsolete by new technology.

        The market for discovery and analysis tools is characterized by rapid technological change and frequent new product introductions. Rapidly changing technology could make some or all of our product lines obsolete unless we are able to continually improve our existing products and develop new products. Because substantially all of our products are based on our core technology platforms, including X-ray technologies, magnetic resonance technologies, mass spectrometry technologies, vibrational spectroscopy and X-ray technology,superconducting magnet technologies, we are particularly vulnerable to any technological advances that would make either certain mass spectrometry, or certain vibrational spectroscopy or certain X-ray analysis toolsof these techniques obsolete as the basis for analytical systems in any of our markets. To meet the evolving needs of our customers, we must rapidly and continually enhance our current and planned products and services and develop and introduce new products and services. In addition, our product lines are

based on complex technologies which are subject to rapid change as new technologies are developed and introduced in the marketplace. We may have difficulty in keeping abreast of the rapid changes affecting each of the different markets we serve or intend to serve. If we fail to develop and introduce products in a timely manner in response to changing technology, market demands or the requirements of our customers, our product sales may decline, and we could experience significant losses.

If we are unable to make or complete future mergers, acquisitions or strategic alliances as a part of our growth strategy, or integrate recent or future mergers, acquisitions or strategic alliances, our business development may suffer.

        Our strategy potentially includes expanding our technology base through selected mergers, acquisitions and strategic alliances. We may seek to continue to expand our technology base through mergers, acquisitions and strategic alliances. If we fail to effect mergers, acquisitions and strategic alliances, our technology base may not expand as quickly and efficiently as possible. Without such complementary growth from selected mergers, acquisitions and strategic alliances, our ability to keep up with the evolving needs of the markets we serve and to meet our future performance goals could be adversely affected. However, we may not be able to find attractive candidates, or enter into mergers, acquisitions or strategic alliances on terms that are favorable to us, or successfully integrate the operations of companies that we acquire. In addition, we may compete with other companies for these merger, acquisition or strategic alliance candidates, which could make such a transaction more expensive for us. If we are able to successfully identify and complete a merger, acquisition or strategic alliance, it could involve a number of risks, including, among others:

•

the difficulty of coordinating or consolidating geographically separate organizations and integrating personnel with different business backgrounds and corporate cultures;



•

the difficulty of integrating previously autonomous departments in accounting and finance, sales and marketing, distribution, and administrative functions, and expanding and integrating information and management systems;



•

the diversion of resources and management time;



•

the potential disruption of our ongoing business;



•

the potential impairment of relationships with customers as a result of changes in management or otherwise arising out of such transactions; and

Table of Contents

•

the significantly increased risk of key management or key employees leaving the acquired companies within the first 1-2 years after the acquisition, including the risk that they may complete with us subsequently.

        If we are not able to successfully integrate acquired businesses, we may not be able to realize all of the cost savings and other benefits that we expect to result from the transactions.

Our business could be harmed if our collaborations fail to advance our product development.

        Demand for our products will depend in part upon the extent to which our collaborations with pharmaceutical, biotechnology and proteomics companies are successful in developing, or helping us to develop, new products and new applications for our existing products. In addition, we collaborate with academic institutions and government research laboratories on product development. We have limited or no control over the resources that any collaborator may devote to our products. Any of our present or future collaborators may not perform their obligations as expected. If we fail to enter into or maintain appropriate collaboration agreements, or if any of these events occur, we may not be able to develop some of our new products, which could materially impede our ability to generate revenue or profits.

We face substantial competition.

        We face substantial competition and we expect that competition in all of our markets will increase further. Currently, our principal competition comes from established companies providing products using existing technologies, including mass spectrometry, X-ray technology, optical emission spectrometry technology, vibrational spectroscopy, CBRNE detection technologies, TD-NMR technologies and other technologies, which perform many of the same functions for which we market our products. Other companies also may choose to enter our fields in the future. Our competitors may develop or market products that are more effective or commercially attractive than our current or future products or that may render our products obsolete. Competition has in the past and is likely in the future to subject our products to pricing pressure. Many of our competitors have more experience in the market and substantially greater financial, operational, marketing and technical resources than we do which could give them a competitive edge in areas such as research and development, production, marketing and distribution. Our ability to compete successfully will depend, in part, on our ability to develop proprietary products that reach the market in a timely manner and are technologically superior to, less expensive than, or more cost-effective than, other currently marketed products.

If we are unable to recover significant development costs of one or more of our products or product lines, our business, results of operations and financial condition may suffer.

        We offer and plan to continue to offer a broad product line and incur and expect to continue to incur substantial expenses for the development of new products and enhanced versions of our existing products. Our business model calls for us to derive a significant portion of our revenues each year from products that did not exist in the previous two years. However, we may experience difficulties which may delay or prevent the successful development, introduction and marketing of new products or product enhancements. The speed of technological change in life science and other related markets we serve may prevent us from successfully marketing some or all of our products for the length of time required to recover their often significant development costs. If we fail to recover the development costs of one or more products or product lines, our business, results of operations and financial condition could be harmed.

Table of Contents

If we lose our strategic partners, our marketing efforts could be impaired.

        A substantial portion of our sales of selected products consists of sales to third parties who incorporate our products in their systems. These third parties are responsible for the marketing and sales of their systems. We face substantial competition.have little or no control over their marketing and sales activities or how they use their resources. Our present or future strategic partners may or may not purchase sufficient quantities of products from us or perform appropriate marketing and sales activities. In addition, if we are unable to maintain our relationships with strategic partners, our business may suffer. Failures by our present or future strategic partners, or our inability to maintain or enter into new arrangements with strategic partners for product distribution, could materially impede the growth of our business and our ability to generate sufficient revenue and profits.

If general health care spending patterns decline, our ability to generate revenue may suffer.

        We face substantial competitionare dependent, both directly and we expect that competitionindirectly, upon general health care spending patterns, particularly in all of our markets will increase further. Currently, our principal competition comes from established companies providing products using existing technologies, including mass spectrometry, X-ray technology, vibrational spectroscopy, CBRN detection technologies and other technologies, which perform many of the same functions for which we market our products. Other companies also may choose to enter our field in the future. In addition, some of our technologies indirectly compete for funding with technologies and products provided by our affiliate Bruker BioSpin; this competition creates the potential for actual or perceived conflicts of interest. Our competitors may develop or market products that are more effective or commercially attractive than our current or future products or that may render our products obsolete. Competition has in the past and is likely in the future to subject our products to pricing pressure. Many of our competitors have more experience in the market and substantially greater financial, operational, marketing and technical resources than we do which could give them a competitive edge in areas such as research and development production, marketingbudgets of the pharmaceutical and distribution. Our abilitybiotechnology industries, as well as upon the financial condition and funding priorities of various governments and government agencies. Since our inception, both we and our academic collaborators and customers have benefited from various governmental contracts and research grants. Whether we or our academic collaborators will continue to compete successfully will depend,be able to attract these grants depends not only on the quality of our products, but also on general spending patterns of public institutions.

Any reduction in part, onthe capital resources or government funding of our customers could reduce our sales and impede our ability to develop proprietary products that reachgenerate revenue.

        A significant portion of our sales are capital purchases by our customers. The spending policies of our customers could have a significant effect on the marketdemand for our products. These policies are based on a wide variety of factors, including the resources available to make purchases, the spending priorities among various types of equipment, policies regarding spending during recessionary periods and changes in the political climate. Any changes in capital spending or changes in the capital budgets of our customers could significantly reduce demand for our products. The capital resources of our life science and other corporate customers may be limited by the availability of equity or debt financing. Any significant decline in research and development expenditures by our life science customers could significantly decrease our sales. In addition, we make a timely mannersubstantial portion of our sales to non-profit and government entities which are technologically superiordependent on government support for scientific research. Any decline in this support could decrease the ability of these customers to less expensive than, or more cost-effective than, other currently marketedpurchase our products.

Our operations are dependent upon a limited number of suppliers and contract manufacturers.

        We currently purchase components used in our mass spectrometry, vibrational spectroscopy and X-ray systemsproducts from a limited number of outside suppliers. Our reliance on a limited number of suppliers could result in time delays associated with redesigning a product due to an inability to obtain an adequate supply of required components and reduced control over pricing, quality and timely delivery. Any of these factors could adversely affect our revenues and profitability. For example, we currently purchase key components used in our mass spectrometry, vibrational spectroscopy and X-ray systems from certain suppliers. In particular, Bruker AXS obtains a sophisticated chip for use in its CCD detectors from Fairchild Imaging which, to Bruker AXS' knowledge, is the only source of a chip of this size and quality. The X-ray microanalysis business of Bruker AXS, which manufactures and sells accessories for electron microscopes, is partially dependent on cooperation from larger manufacturers of electron microscopes. Additionally, Bruker Daltonics purchases certain magnets from a single supplier, Varian/Magnex, and also obtains certain key components for the manufacture of its ion traps

from Agilent, the sole supplier of these components. Our Bruker-QuantronBruker-Elemental subsidiary purchases certain optical detectors from a single supplier, PerkinElmer, Inc., the sole supplier of certainthese detector components. Bruker Optics purchases its

Table of Contents

focal plane array detectors from a single supplier, Lockheed Martin Corporation. Similarly, Bruker BioSpin obtains various components from sole or limited source suppliers and Bruker Advanced Supercon obtains various raw materials and key production equipment from sole or limited source suppliers. There are limited, if any, available alternatives to these suppliers. The existence of shortages of these components or the failure of delivery with regard to these components could have a material adverse effect upon our revenues and margins. In addition, price increases from these suppliers could have a material adverse effect upon our gross margins.

        Because of the scarcity of some components, we may be unable to obtain an adequate supply of components, or we may be required to pay higher prices or to purchase components of lesser quality. Any delay or interruption in the supply of these or other components could impair our ability to manufacture and deliver our products, harm our reputation and cause a reduction in our revenues. In addition, any increase in the cost of the components that we use in our products could make our products less competitive and decrease our gross margins. We may not be able to obtain sufficient quantities of required components on the same or substantially the same terms. Additionally, consolidations among our suppliers could result in other sole source suppliers for us in the future.

Our businessIncreasing prices of metal raw materials and superconducting wire could be harmed ifadversely affect the gross margins and profitability of our collaborations fail to advanceBruker BioSpin subsidiary, and of our product development.Bruker Advanced Supercon business.

        DemandThe last few years have seen sharp increases in the prices for our products will dependvarious raw materials, in part upondue to high demand from developing countries. Both Bruker BioSpin and Bruker Advanced Supercon rely on some of these materials for the extent to which our collaborations with pharmaceutical, biotechnologyproduction of their products. In particular, for its superconducting magnet production, both for the horizontal and proteomics companies are successful in developing, or helping us to develop, new productsvertical magnet series, Bruker BioSpin relies on the availability of copper, steel and new applicationsthe metallic raw materials for our existingtraditional low-temperature superconducting wires. Higher prices for these commodities will increase the production cost of superconducting wires and superconducting magnets and may adversely affect gross margins.

        The prices of copper and certain other raw materials used for superconductors have increased significantly over the last decade. Since copper is a main constituent of low temperature superconductors, this may affect the price of superconducting wire. This type of increase would have an immediate effect on the production costs of superconducting magnets and may negatively affect the profit margins for those products. In addition, we collaborate with academic institutionsan increase in raw material cost affects the production cost of the superconducting wire produced by Bruker Advanced Supercon and government research laboratories on product development. We have limited or no controlof superconducting wire used by Bruker BioSpin.

The emerging risk of liquid helium becoming scarce and significantly more expensive could dampen the demand for NMR, EPR, MRI and FTMS products.

        The demand for helium has risen sharply over the resources that any collaboratorlast decade. The superconducting magnets used in magnetic resonance rely on liquid helium for their operation. The high global demand, in combination with a shortage in supply, has caused prices for liquid helium to rise significantly. This has an adverse effect on the operating costs for magnetic resonance equipment, and may devotedampen demand for NMR, EPR, MRI and FTMS magnets in the future.

Our manufacture and sale of products could lead to our products. Anyproduct liability claims for which we could have substantial liability.

        The manufacture and sale of our present or future collaborators may not perform their obligations as expected. If we failproducts exposes us to enter into or maintain appropriate collaboration agreements, orproduct liability claims if any of our products cause injury or are found otherwise unsuitable during manufacturing, marketing, sale or customer use. In particular, if one of our CBRNE detection products malfunctions, this could lead to civilian or military casualties in a time of unrest, exposing us to increased potential for high-profile liability. If our CBRNE detection products malfunction by generating a false-positive to a potential

Table of Contents

threat, we could be exposed to liabilities associated with actions taken that otherwise would not have been required. Additionally, the nuclear magnetic resonance, research magnetic resonance imaging, Fourier transform mass spectrometry and certain electron paramagnetic resonance magnets of Bruker BioSpin utilize high magnet fields and cryogenics to operate at approximately 4 Kelvin, the temperature of liquid helium. There is an inherent risk of potential product liability due to the existence of these events occur, wehigh magnetic fields, associated stray fields outside the magnet, and the handling of the cryogens associated with superconducting magnets. In addition, the Bruker Daltonics MALDI Biotyper has an IVD-CE mark and is used for the identification of microorganisms. Misidentification or a false-negative of certain bacteria, yeasts or fungi could lead to inappropriate treatment for patients, and could expose Bruker Daltonics to product liability.

        A successful product liability claim brought against us in excess of, or outside the coverage of, our insurance coverage could have a material adverse effect on our business, financial condition and results of operations. We may not be able to develop some of our new products, which could materially impede our ability to generate revenue or profits.maintain product liability insurance on acceptable terms, if at all, and insurance may not provide adequate coverage against potential liabilities.

IfResponding to claims relating to improper handling, storage or disposal of hazardous chemicals and radioactive and biological materials which we lose our strategic partners, our marketing effortsuse could be impaired.time consuming and costly.

        A substantial portion of our sales of selected products consists of sales to third parties who incorporate our productsWe use controlled hazardous and radioactive materials in their systems. These third parties are responsible for the marketing and sales of their systems. We have little or no control over their marketing and sales activities or how they use their resources. Our present or future strategic partners may or may not purchase sufficient quantities of products from us or perform appropriate marketing and sales activities. In addition, if we are unable to maintain our relationships with strategic partners, our business may suffer. Failures by our present or future strategic partners, or our inability to maintain or enter into new arrangements with strategic partners for product distribution, could materially impede the growth of our business and our ability to generate sufficient revenuewastes that are regulated as hazardous wastes under United States federal, and profits.

If we are unable to make or complete future mergers, acquisitions or strategic alliances as a partMassachusetts, California and Wisconsin state, environmental and atomic energy regulatory laws and under equivalent provisions of our growth strategy or integrate recent or future mergers, acquisitions or strategic alliances, our business development may suffer.

        Our strategy includes potentially expanding our technology base through selected mergers, acquisitions and strategic alliances. In 2005, our indirect subsidiary, Bruker AXS GmbH, acquired Roentec AG, an X-ray microanalysis instrumentation company basedlaw in Berlin, Germany, andthose jurisdictions in which our direct subsidiary, Bruker AXS, acquired the microanalysis business of Princeton Gamma-Tech Instruments, Inc., a company located in Rocky Hill, New Jersey. The acquired businesses were combined to form a new group within Bruker AXS that focuses on the microanalysis market, a market not previously addressed by Bruker AXS. In the first quarter of 2006, Bruker AXS GmbH completed its acquisition of Socabim SAS, a privately-held Paris, France based company focused on advanced X-ray materials research and analysis software. On July 1, 2006,manufacturing facilities are located. Our use of these substances and materials is subject to stringent, and periodically changing, regulation that can impose costly compliance obligations on us and have the potential to adversely affect our manufacturing activities. The risk of accidental contamination or injury from these materials cannot be completely eliminated. If an accident with these substances occurs, we completed our acquisition of Bruker Optics. On July 18, 2006, Bruker AXS acquired KeyMaster Technologies, Inc., a developer and manufacturer of portable hand-held X-ray fluorescence (XRF) systems located in Kennewick, Washington. On September 6, 2006, Bruker AXS GmbH completed its acquisition of Quantron GmbH, an optical emission spectroscopy company based in Kleve, Germany.

        We may seek to continue to expand our technology base through mergers, acquisitions and strategic alliances. If we fail to effect mergers, acquisitions and strategic alliances, our technology base may not expand as quickly and efficiently as possible. Without such complementary growth from selected mergers, acquisitions and strategic alliances, our ability to keep up with the evolving needs of the markets we serve and to meet our future performance goals could be adversely affected. However, we may not be able to find attractive candidates, or enter into mergers, acquisitions or strategic alliances on termsheld liable for any damages that are favorable to us, or successfully integrate the operations of companies that we acquire. In addition, we may compete with other companies for these merger, acquisition or strategic alliance candidates, which could make such a transaction more expensive for us. If we are able to successfully identify and complete a merger, acquisition or strategic alliance, it could involve a number of risks, including, among others:

•

the difficulty of coordinating or consolidating geographically separate organizations and integrating personnel with different business backgrounds and corporate cultures;



•

the difficulty of integrating previously autonomous departments in accounting and finance, sales and marketing, distribution, and administrative functions, and expanding and integrating information and management systems;



•

the diversion of resources and management time;



•

the potential disruption of our ongoing business; and



•

the potential impairment of relationships with customers as a result, of changes in management or otherwise arising out of such transactions.

If we are not able to successfully integrate acquired businesses, we may not be able to realize all of the cost savings and other benefits that we expect to result from the transactions.

Goodwill and other intangible assets are subject to impairment.

        As a result of the merger of Bruker Daltonics and Bruker AXS in July 2003, we recorded goodwill and other intangible assets, which must be periodically evaluated for potential impairment. In addition, the recent acquisitions of Roentec, Socabim, Bruker Optics, KeyMaster and Quantron and the microanalysis business of Princeton Gamma-Tech Instruments resulted in additional goodwill and other intangible assets. We assess the realizability of the goodwill and other intangible assets annually as well as whenever events or changes in circumstances indicate that the assets may be impaired. These events or circumstances generally include operating losses or a significant decline in the earnings associated with the business segment these acquisitions are reported within. Our ability to realize the value of the goodwill will depend on the future cash flows of the business segment in addition to how well we integrate the businesses.incurring clean-up costs and liabilities, which can be substantial. Additionally, an accident could damage our research and manufacturing facilities resulting in delays and increased costs.

In addition to the risks applicable to our life science and materials analysis products, our CBRNCBRNE detection products are subject to a number of additional risks, including lengthy product development and contract negotiation periods and certain risks inherent in long-term government contracts; our Fourier Transform Infrared, or FTIR, business with the Chinese State Food and Drug Administration, or SFDA, is also subject to the risks inherent in long-term government contracts.

        Our CBRNCBRNE detection products are subject to many of the same risks associated with our life science products, including vulnerability to rapid technological change, dependence on mass spectrometry and other technologies and substantial competition. In addition, our CBRNCBRNE detection products as well as our FTIRand FT-IR products are generally sold to government agencies under long-term contracts. These contracts generally involve lengthy pre-contract negotiations and product development. We may be required to devote substantial working capital and other resources prior to obtaining product orders. As a result, we may incur substantial costs before we recognize revenue from these products. Moreover, in return for larger, longer-term contracts, our customers for these products often demand more stringent acceptance criteria. TheirThese criteria may also cause delays in our ability to

recognize revenue from sales of these products. Furthermore, we may not be able to accurately predict in advance our costs to fulfill our obligations under these long-term contracts. If we fail to accurately predict our costs, due to inflation or other factors, we could incur significant losses. Any single long-term contract for our FTIR products, such as Bruker Optics' existing contract with the Chinese SFDA, or for our CBRN detection products, may represent a material portion of our total business volume, and the loss of any such contract could have a material adverse effect on our results of operations. Failure to increase other business or to obtain additional government contracts could cause our revenue to decline. Also, the presence or absence of such contracts may cause substantial variation in our results of operations between fiscal periods and, as a result, our results of operations for any given fiscal period may not be predictive of our results for subsequent fiscal periods. The resulting uncertainty may have an adverse impact on our stock price.

If general health care spending patterns decline, our ability to generate revenue may suffer.

        We are dependent, both directly and indirectly, upon general health care spending patterns, particularly in the research and development budgetsTable of the pharmaceutical and biotechnology industries, as well as upon the financial condition of various governments and government agencies. Since our inception, both we and our academic collaborators and customers have benefited from various governmental contracts and research grants. Whether we or our academic collaborators will continue to be able to attract these grants depends not only on the quality of our products, but also on general spending patterns of public institutions. The proposed federal budget for fiscal year 2007 freezes spending for the National Institute of Health (NIH) at $28.6 billion. Such a freeze or a potential decrease in the level of governmental spending allocated to scientific and medical research could substantially reduce or even eliminate our grants as well as decrease demand for our products from academic and medical research customers, many of which receive funding from NIH.

Any reduction in the capital resources or government funding of our customers could reduce our sales and impede our ability to generate revenue.Contents

        A significant portion of our sales are capital purchases by our customers. The spending policies of our customers could have a significant effect on the demand for our products. These policies are based on a wide variety of factors, including the resources available to make purchases, the spending priorities among various types of equipment, policies regarding spending during recessionary periods and changes in the political climate. Any changes in capital spending or changes in the capital budgets of our customers could significantly reduce demand for our products. The capital resources of our biotechnology and other corporate customers may be limited by the availability of equity or debt financing. Any significant decline in research and development expenditures by our life science customers could significantly decrease our sales. In addition, we make a substantial portion of our sales to non-profit and government entities which are dependent on government support for scientific research. Any decline in this support could decrease the ability of these customers to purchase our products.

We are subject to existing and potential additional regulation and government inquiry, which can impose burdens on our operations and narrow the markets for our products.

        We are subject, both directly and indirectly, to the adverse impact of existing and potential future government regulation of our operations and markets. For example, exportation of our products, particularly our CBRNCBRNE detection products, is subject to strict regulatory control in a number of jurisdictions. The failure to satisfy export control criteria or obtain necessary clearances could delay or prevent shipment of products, which could adversely affect our revenues and profitability. Moreover, the life sciences industry, which is the market for our principal products, has historically been heavily regulated. There are, for example, laws in several jurisdictions restricting research in genetic engineering, which can operate to narrow our markets. Given the evolving nature of this industry,

        The current world unrest, or the responses of the United States, may lead to further acts of terrorism and civil disturbances in the United States or elsewhere, which may further contribute to the economic instability in the United States. These attacks or armed conflicts may affect our physical facilities or those of our suppliers or customers and could have an impact on our domestic and international sales, our supply chain, our production capability, our insurance premiums or the ability to purchase insurance and our ability to deliver our productsRisks Related to our customers. The consequences of these risks are unpredictable, and their long-term effect upon us is uncertain.Common Stock

The unpredictability and fluctuation of our quarterly results may adversely affect the trading price of our common stock.

        Our revenues and results of operations have in the past and may in the future vary from quarter to quarter due to a number of factors, many of which are outside of our control and any of which may cause our stock price to fluctuate. The primary factors that may affect us include the following:

•

the timing of sales of our products and services;



•

the timing of recognizing revenue and deferred revenue under U.S. GAAP;



•

changes in our pricing policies or the pricing policies of our competitors;



•

increases in sales and marketing, product development or administration expenses;



•

the mix of services provided by us and third-party contractors;



•

our ability to attain and maintain quality levels for our products;



•

costs related to acquisitions of technology or businesses; and



•

the effectiveness of transactions entered into to hedge the risks associated with foreign currency and interest rate fluctuations.

        Historically, we have experienced a decrease in revenue in the first, second and third quarters of each fiscal year relative to the prior fourth quarter, which we believe is due to our customers' budgeting cycles. These seasonal fluctuations may increase in the future as a result of the acquisition of Bruker BioSpin in February 2008. You should not rely on quarter-to-quarter comparisons of our results of operations as an indication of our future performance. It is likely that in some future quarters, our results of operations may be below the expectations of public market analysts and investors. In this event, the price of our common stock may fall.

We face potential volatility of our stock price.

        There has only been a public market for our common stock since August 2000. The market price of our common stock may fluctuate substantially in response to various factors, many of which are beyond our control, including:

•

quarterly fluctuations in results of operations, as described above;



•

our ability to successfully commercialize our products;



•

technological innovations or new commercial products by us or our competitors;



•

developments concerning government regulations or proprietary rights which could affect the potential growth of our markets;



•

material changes in our relationships with, or the viability of, strategic business partners;



•

market reaction to trends in revenues and expenses, especially research and development;



•

changes in earnings estimates by analysts;



•

volatility and uncertainty in the capital markets in general;



•

loss of key personnel;



•

changes in accounting principles;



•

lack of trading volume in our stock;



•

fluctuation within the life science and industrial analysis markets;



•

sales of common stock by existing stockholders, particularly large institutional investors who cannot hold stock traded at less than $5 per share; and



•

economic and political conditions.

        The market price for our common stock may also be affected by our ability to meet analysts' expectations. Any failure to meet such expectations, even slightly, could have an adverse effect on the market price of our common stock. In addition, the stock market, the Nasdaq Global Market and the market for life science stocks in particular, has been and is subject to extreme price and volume fluctuations. This volatility has had a significant effect on the market prices of securities issued by many companies for reasons unrelated to the operating performance of these companies. In the past, companies that have experienced volatility in the market price of their securities have been the subjects of securities class action litigation. Any such litigation instigated against us could result in substantial costs and a diversion of managements' attention and resources, which could significantly harm our business, financial condition and operating results.

Certain financial information incorporated by reference in this prospectus is presented on a basis different from the basis on which our most recently published financial information is presented and is therefore not comparable.

        We have incorporated by reference in this prospectus financial statements and other financial information that do not include the financial position and results of operations of Bruker Optics and Bruker BioSciences as a consolidated entity. These financial statements complied with applicable accounting requirements when they were initially filed and are incorporated by reference herein in accordance with the rules and regulations of the Securities and Exchange Commission. Our most recently published financial information is presented on a combined basis and includes the financial position and results of operations of Bruker Optics and Bruker BioSciences as if they had been a part of a consolidated entity for all periods presented, even as to periods prior to the Bruker Optics

acquisition. This presentation also complies with applicable accounting requirements. As a result of the different bases of presentation, however, the financial statements and other financial information published more recently are not comparable to the financial statements and other financial information that excludes the combined financial position and results of operations of Bruker Optics and Bruker BioSciences, and the latter should not be relied upon in assessing our financial performance or in making an investment decision with respect to this offering. For more information, see "Cautionary Note Regarding Financial Information."

Future sales of our stock may impact its market price.

        Sales of substantial numbers of shares of our common stock in the public market, or the perception that significant sales are likely, could adversely affect the market price of our common stock. The number of shares of common stock covered by this prospectus, including the underwriters' overallotment option, is equal to approximately 11.7% of the currently outstanding shares of our common stock. We cannot predict the effect that market sales of such a large number of shares would have on the market price of our common stock.

Existing stockholders have significant influence over us.

        Our LaukienAs of June 11, 2009, our majority stockholders, including the selling stockholdersour Chairman, President and Chief Executive Officer Frank H. Laukien, own or control,Director and Senior Vice President Dirk Laukien, Director and Chief Operating Officer of Bruker BioSpin Joerg Laukien and other Laukien family members owned, in the aggregate, approximately 62.5%69% of our outstanding common stock (approximately 53.3% upon completion of this offering, or 52.0% if the overallotment option is exercised in full).stock. As a result, these stockholders will be able to exercise substantial influence over all matters requiring stockholder approval, including the election of directors and approval of significant corporate transactions. This could have the effect of delaying or preventing a change in control of our company and will make some transactions difficult or impossible to accomplish without the support of these stockholders.

Table of Contents

Other companies may have difficulty acquiring us, even if doing so would benefit our stockholders, due to provisions under our corporate charter and bylaws, and as well as Delaware law.

        Provisions in our certificate of incorporation, as amended, and our bylaws, as well as Delaware law could make it more difficult for other companies to acquire us, even if doing so would benefit our stockholders. Our certificate of incorporation, as amended, and bylaws contain the following provisions, among others, which may inhibit an acquisition of our company by a third party:

•

staggered board of directors, where stockholders elect only a minority of the board each year;



•

advance notification procedures for matters to be brought before stockholder meetings;



•

a limitation on who may call stockholder meetings; and



•

the ability of our board of directors to issue up to 5,000,000 shares of preferred stock without a stockholder vote.

Management will have broad discretion as to the useFuture or anticipated sales of the proceeds received by us from this offering, and weour stock may not use the proceeds effectively.impact its market price.

        We have not designatedSales of substantial numbers of shares of our common stock in the amountpublic market, or the perception that significant sales are likely, could adversely affect the market price of net proceeds we will use for any particular purpose. Accordingly, our management will have broad discretion ascommon stock. The number of shares of common stock covered by this prospectus is equal to the applicationapproximately 43% of the net proceeds andcurrently outstanding shares of our common stock. We cannot predict the effect that market sales of such a large number of shares would have on the market price of our common stock. Moreover, actual or anticipated downward pressure on the market price of our common stock due to actual or anticipated sales of our common stock could use them for purposes other than those contemplated atcause some institutions or individuals to engage in short sales of our common stock, which may itself cause the timemarket price of this offering. Our stockholders may not agree with the manner in which our management choosescommon stock to allocate and spend the net proceeds. Moreover, our management may use the net proceeds for corporate purposes that may not increase our market value or make us profitable.

decline.

USE OF PROCEEDS

        We estimate thatExcept as otherwise may be described in the applicable prospectus supplement accompanying this prospectus, we expect to add substantially all of the net proceeds from the sale of the 2,200,000offered primary shares of common stock we are offeringto our general funds. These funds will be approximately $16.2 million after deducting underwriting discounts and commissions, and the estimated offering expenses payable by us, based on an assumed public offering price of $7.92 per share. If the underwriters exercise their over-allotment option in full, we estimate that the net proceeds to us will be approximately $18.7 million. Each $1.00 increase (decrease) in the assumed offering price of $7.92 per share would increase (decrease) the net proceeds to us from this offering by approximately $2.1 million, assuming that the number of shares offered by us, as set forth on the cover page of this prospectus, remains the same. Depending on market conditions at the time of pricing of this offering and other considerations, we may sell fewer or more shares than the number set forth on the cover page of this prospectus.

        We intend to use the net proceeds from our sale of common stock in this offeringused for general corporate purposes, potential acquisitions complementary to our existing businessincluding capital expenditures, repayment of long term and short term debt, working capital and the repaymentfinancing of some of our debt. Specifically, wefuture acquisitions. We may repay a portion of the outstanding amount on our line of credit with Citizens Bank. In July 2006, we issued a demand promissory note for a $40 million line of credit with Citizens Bank. In July 2006, we borrowed $20 million on this line of credit to finance a portion of our acquisition of Bruker Optics and an additional $10 million to finance our purchase of KeyMaster Technologies, Inc. During the third quarter of 2006, we repaid $10 million outstanding on this line of credit and on December 13, 2006 repaid an additional $3 million. The note bears interest at the bank's prime rate, LIBOR plus 1%, or, at our request, a LIBOR advantage rate plus 1%. As of December 14, 2006, we owed $17 million on this line of credit.

        As of the date of this prospectus, we cannot specify with certainty all of the particular uses for the net proceeds we will have upon completion of the offering. Accordingly, we will retain broad discretion over the use of these proceeds. Pending the use of the net proceeds, we intend toalso invest the net proceedsfunds which are not required immediately in short-term interest-bearing, investment-grademarketable securities.

        We will not receive any proceeds from the sale of secondary shares of common stock by the selling stockholders.

PRICE RANGE OF COMMON STOCK

        Our common stock has traded on the Nasdaq Global Market since August 4, 2000, the date that our common stock was first offered to the public. Prior to our merger with Bruker AXS Inc., our common stock traded under the symbol "BDAL." Since the consummation of the merger on July 1, 2003, our common stock has traded under the symbol "BRKR." The following table sets forth on a per share basis the high and low sales prices for our common stock for the quarters indicated. Prices shown are from the Nasdaq Global Market.

        On December 12, 2006, the reported last sale price for our common stock on the Nasdaq Global Market was $7.98 per share. Investors should obtain current market quotations before making any decision with respect to an investment in our securities.

        On December 12, 2006, there were 102,345,906 shares of our common stock outstanding, held by approximately 99 stockholders of record. This number does not include the individual beneficial owners of shares held in nominee name or within clearinghouse positions of brokerage firms and banks.

DIVIDEND POLICY

        We have not declared or paid any dividends on our common stock since our inception and do not intend to pay any dividends on our common stock in the foreseeable future. We currently intend to retain available funds for use in our business. Any determination to pay dividends in the future will be at the discretion of our board of directors and will depend upon, among other things, our financial condition, results of operations and capital requirements. The terms of some of our outstanding indebtedness prohibit us from paying cash dividends.

CAPITALIZATION

        The following table sets forth our capitalization as of September 30, 2006:

•

on an actual basis; and



•

as adjusted to reflect the receipt and application by us of the estimated net proceeds from our sale of 2,200,000 shares of our common stock in this offering, at an assumed public offering price of $7.92 per share, after deducting underwriting discounts and commissions and the estimated offering expenses.

        You should read this table in conjunction with the financial statements and the other financial information and "Management's Discussion and Analysis of Financial Condition and Results of Operations" included or incorporated by reference elsewhere in this prospectus.

        The table above does not include:

•

3,038,609 shares of common stock issuable upon exercise of options outstanding at a weighted average exercise price of $6.72 per share at September 30, 2006; and



•

3,369,433 additional shares of common stock available for future grant under our 2000 Stock Option Plan at September 30, 2006.

(1)

Each $1.00 increase (decrease) in the assumed public offering price of $7.92 per share would increase (decrease) each of cash and cash equivalents, additional paid-in capital, total stockholders' equity and total capitalization by approximately $2.1 million, assuming that the number of shares offered by us, as set forth on the cover page of this prospectus, remains the same. Depending on market conditions at the time of pricing of this offering and other considerations, we may sell fewer or more shares than the number set forth on the cover page of this prospectus. The as adjusted information discussed above is illustrative only and following the completion of this offering will be adjusted based on the actual public offering price and other terms of this offering determined at pricing.

DESCRIPTION OF COMMON STOCK

        The following summary of our common stock does not purport to be complete. You should read the applicable provisions of Delaware General Corporation Law, our certificate of incorporation and our by-laws. This summary is qualified in its entirety by reference to the provisions of our certificate of incorporation, as amended, and by-laws, which have been filed with the Securities and Exchange Commission.

General

        We are authorized to issue 200,000,000 shares of common stock, par value $.01 per share, and 5,000,000 shares of undesignated preferred stock, par value $.01 per share.

        As of December 12, 2006, 102,345,906 shares of our common stock were issued and outstanding, no shares of our preferred stock were issued and outstanding and 3,582,640 shares of our common stock were reserved for issuance under our stock option plan.

        Holders of our common stock are entitled to one vote for each share held on all matters submitted to a vote of the stockholders, including the election of directors. Accordingly, holders of a majority of the shares of common stock entitled to vote in any election of directors may elect all of the directors standing for election if they choose to do so. Our certificate of incorporation does not provide for cumulative voting for the election of directors. Holders of our common stock are entitled to receive ratably any dividends that may be declared by the board of directors out of funds legally available and are entitled to receive, pro rata, all of our assets available for distribution to such holders upon liquidation. Holders of our common stock have no preemptive, subscription or redemption rights.

Anti-Takeover Effects of Certain Provisions of Our Certificate of Incorporation, Bylaws and Stock Option Plan

        Certificate of Incorporation and Bylaws Provisions.    Our certificate of incorporation and bylaws include provisions that may have the effect of discouraging, delaying or preventing a change in control or an unsolicited acquisition proposal that a stockholder might consider favorable, including a proposal that might result in the payment of a premium over the market price for the shares held by stockholders. These provisions are summarized in the following paragraphs.

        Classified Board of Directors.    Our certificate of incorporation and bylaws provide for our board to be divided into three classes of directors serving staggered, three year terms. The classification of the board has the effect of requiring at least two annual stockholder meetings, instead of one, to replace a majority of the members of the board of directors.

        Authorized but Unissued or Undesignated Capital Stock.    Our authorized capital stock consists of 200,000,000 shares of common stock and 5,000,000 shares of preferred stock. The authorized but unissued (and in the case of preferred stock, undesignated) stock may be issued by the board of directors in one or more transactions. In this regard, our amended and restated certificate of incorporation grants the board of directors broad power to establish the rights and preferences of authorized and unissued preferred stock. The issuance of shares of preferred stock pursuant to the board of directors' authority described above could decrease the amount of earnings and assets available for distribution to holders of common stock and adversely affect the rights and powers, including voting rights, of such holders and may have the effect of delaying, deferring or preventing a change in control. The board of directors does not currently intend to seek stockholder approval prior to any issuance of preferred stock, unless otherwise required by law.

        Special Meetings of Stockholders.    Our bylaws provide that special meetings of our stockholders may be called only by our board of directors, by our Chairman of the board of directors or by our

President. In addition, the President or Secretary shall call a special meeting if requested by a majority of directors.

        Notice Procedures.    Our bylaws establish advance notice procedures with regard to all stockholder proposals to be brought before meetings of our stockholders, including proposals relating to the nomination of candidates for election as directors, the removal of directors and amendments to our certificate of incorporation or bylaws. These procedures provide that notice of such stockholder proposals must be timely given in writing to our Secretary prior to the meeting. Generally, to be timely, notice must be received at our principal executive offices no later than the close of business on the 90^th day nor earlier than the close of business on the 120^th day prior to the date set forth in the bylaws for the annual meeting. The notice must contain certain information specified in the bylaws.

        Other Anti-Takeover Provisions.    Our Amended and Restated 2000 Stock Option Plan contains provisions which may have the effect of discouraging, delaying or preventing a change in control or unsolicited acquisition proposals. In the event of any (i) sale or conveyance to another entity of all or substantially all of our property and assets, including, without limitation, by way of merger or consolidation, or (ii) change of control, the purchaser may, in his, her or its discretion, deliver to the optionee the same kind of consideration that is delivered to the shareholders as a result of such sale, conveyance or change in control, or the board of directors may cancel all outstanding options in exchange for consideration in cash or in kind equal to the value of those shares of stock the optionee would have received had the option been exercised (to the extent exercisable) and no disposition of the shares has been made prior to such transaction. Upon receipt of such consideration by the optionee, his or her option shall immediately terminate. The board of directors also has the power and right to accelerate the exercisability of any options upon such sale, conveyance or change in control.

        Limitation of Director Liability.    Our certificate of incorporation and bylaws limit the liability of our directors (in their capacity as directors but not in their capacity as officers) to us or our stockholders. Specifically, our certificate of incorporation provides that our directors will not be personally liable for monetary damages for breach of a director's fiduciary duty as a director, except for liability:

•

for any breach of the director's duty of loyalty to us or our stockholders;



•

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



•

under Section 174 of the Delaware General Corporation Law, which relates to unlawful payments of dividends or unlawful stock repurchases or redemptions; or



•

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

        Indemnification Arrangements.    Our bylaws provide that our directors and officers shall be indemnified and provide for the advancement to them of expenses in connection with actual or threatened proceedings and claims arising out of their status as such to the fullest extent permitted by the Delaware General Corporation Law.

Transfer Agent and Registrar

        The transfer agent and registrar for our common stock is American Stock Transfer & Trust Company.

SELLING STOCKHOLDERS

        We are registering for resale certain shares of our common stock. The term "selling stockholder" includes the stockholders listed below and their transferees, pledges, donees or other successors. Each of the selling stockholders may sell some, all or none of his or her shares of common stock that may be offered under this prospectus and is under no obligation to sell any of his or her shares.

        Our five largest stockholders are Frank H. Laukien, Dirk D. Laukien, Isolde Laukien-Kleiner, JörgJoerg C. Laukien and Marc M. Laukien. Dirk Laukien, Isolde Laukien-Kleiner Jörg Laukien and Marc Laukien are the selling stockholders in this offering. Dirk Laukien is a director and Senior Vice President of Bruker BioSciences and the President of our Bruker Optics. Jörg Laukien is a member of the Board of Directors of Bruker BioSciences.Optics subsidiary. Isolde Laukien-Kleiner and Marc Laukien are not actively involved with Bruker, BioSciences, and are not employees, members of management or directors of Bruker BioSciences.Bruker. Frank H. Laukien, our Chairman, President and Chief Executive Officer, isand Joerg Laukien, a director and Chief Operating Officer of our Bruker BioSpin subsidiary, are not sellingregistering any shares of common stock infor resale under this offering.prospectus.

        AsTable of December 12, 2006, the four selling stockholders held, in the aggregate, 44,896,300 shares, or 43.9% of our outstanding common stock. They intend to sell 8,200,000 of those shares in this offering. Upon completion of this offering, these selling stockholders will own 35.1% of our common stock, or 33.8% if the underwriters' overallotment option is exercised in full, and our public float will increase from 37.7% to 46.8% of our outstanding common stock, or 48.2%, if the underwriters' overallotment option is exercised in full. We will not receive any proceeds from the sale of shares by the selling stockholders in this offering.Contents

        Based solely upon information furnished to us by the selling stockholders, the following table sets forth the name of each selling stockholder and, as of December 12, 2006,June 11, 2009, the number and percentage of shares of common stock beneficially owned by each selling stockholder and the number of shares being registered for sale by each selling stockholder. Except as indicated in the footnotes to this table, the persons named in the table have sole voting and investment power with respect to all shares of common stock shown as beneficially owned by them. You should keepconsider the following points in mind as you read the information in the table:

•

The amounts and percentage of our common stock beneficially owned by a holder are reported on the basis of the regulations of the SEC that govern the determination of beneficial ownership of securities. Under these regulations, a person or group of persons is deemed to be a "beneficial owner" of a security if that person or group has or shares "voting power," which includes the power to vote or to direct the voting of the security, or "investment power," which includes the power to dispose of or to direct the disposition of the security. In addition, a person is deemed to be the beneficial owner of securities that can be acquired by such person within 60 days from the applicable date, whether upon the exercise of options or otherwise.



•

The percentage of our common stock outstanding before the offering is based on 102,345,906164,083,675 shares of our common stock outstanding as of December 12, 2006,June 11, 2009, and the percentage of our

common stock outstanding after the offering assumes the sale by us of 2,200,000all 35,000,000 newly issued primary shares of our common stock inthat may be offered under this offering.

prospectus.


•
The number of shares and percentage of outstanding common stock to be owned by the selling stockholders after completion of this offering assumes that each selling stockholders will sell all of his or her shares of common stock registered for resale under this prospectus.

(1)

Includes 41,293 shares of common stock held by the Dirk D. Laukien Trust for Leah Laukien, dated June 1, 2000.2000

        We and the selling stockholders have granted to the underwriters an over-allotment option as described in "Underwriting." The following table sets forth, as to each selling stockholder, the number of shares subject to the underwriters' over-allotment option as well as the number of shares owned by each selling stockholder and the percentage ownership of each selling stockholder after this offering, assuming the exercise in full of the underwriters' over-allotment option:

(1)

Includes 41,293 shares of common stock held by the Dirk D. Laukien Trust for Leah Laukien, dated June 1, 2000.

Certain Relationships

        Our five largest stockholders are Frank H. Laukien, Dirk Laukien, Isolde Laukien-Kleiner, Jörg Laukien and Marc Laukien. Isolde Laukien-Kleiner is the mother of Dirk and Marc Laukien. Jörg,

Frank, Dirk and Marc are brothers or half-brothers. As described above, Dirk Laukien, Isolde Laukien-Kleiner, Jörg Laukien and Marc Laukien are the selling stockholders in this offering and Frank H. Laukien, our Chairman, President and Chief Executive Officer, is not selling any sharesTable of common stock in this offering. Dirk Laukien is a Senior Vice President of Bruker BioSciences and the President of Bruker Optics. Jörg Laukien is a member of the Board of Directors of Bruker Biosciences. Isolde Laukien-Kleiner and Marc Laukien are not actively involved with Bruker BioSciences, and are not employees, members of management or directors of Bruker BioSciences.

        We are affiliated with Bruker BioSpin Inc., Bruker Physik AG, Bruker BioSpin Invest AG, Techneon AG, and their respective subsidiaries, which we refer to collectively as the Bruker BioSpin group, through common control at the stockholder level. Our five largest stockholders are also the controlling stockholders of the Bruker BioSpin group. We also do business with these entities, including product collaborations and distribution and supply arrangements.

        Jörg C. Laukien, a director of Bruker BioSciences, is a director and President of Bruker BioSpin MRI, Inc., President of Bruker Elektronic GmbH, a director of Bruker Biospin Inc., a director of Bruker BioSpin SA, a director of Bruker BioSpin s.r.l., and a director of Techneon AG. Additionally, Jörg Laukien beneficially owns directly or indirectly more than 10% of the stock of each of the Bruker affiliated companies.

        Dirk D. Laukien, President of Bruker Optics, is also Co-President and director of Bruker BioSpin Inc., and a director of Bruker AG, each a Bruker affiliated company. Additionally, Dirk Laukien owns directly or indirectly more than 10% of the stock of each of the Bruker affiliated companies. Bruker Optics rents various office spaces from Dirk Laukien under lease agreements. Under these lease agreements, during each of the years ended December 31, 2005, 2004 and 2003, Dirk Laukien was paid $300,000, which was estimated to be equal to the estimated fair market value less the cost of certain capital improvements provided by Bruker Optics in 2004. Bruker Optics subleased a portion of this office space to an affiliate during 2005, 2004 and 2003 and received $31,500, $100,000 and $200,000 in rental income, respectively, which included charges for utilities and other occupancy costs. In July 2004, Bruker Optics borrowed $1.5 million from Dirk Laukien at a fixed rate of 4.68% due in July 2006. During 2005, this loan was repaid in full.

        Marc Laukien owns directly or indirectly more than 10% of the stock of each of the Bruker affiliated companies.

Contents

UNDERWRITINGPLAN OF DISTRIBUTION

        Either we or any selling stockholder may sell the common stock in one or more of the following ways from time to time:

•

through agents to the public or to investors;



•

to dealers or underwriters for resale to the public or to investors;



•

directly to investors; or



•

through a combination of any of these methods of sale.

We will set forth in a prospectus supplement the terms of that particular offering of common stock, including:

•

the name or names of any agents or underwriters;



•

the purchase price of the common stock being offered and the net proceeds we or the selling stockholders arewill receive from the sale;



•

any over-allotment options under which underwriters may purchase additional shares from us or the selling stockholders;



•

any agency fees or underwriting discounts and other items constituting agents' or underwriters' compensation;



•

the initial public offering price; and



•

any discounts or concessions allowed or reallowed or paid to dealers.

        The selling stockholders also may resell all or a portion of the common stock in open market transactions in reliance upon Rule 144 under the Securities Act.

Agents

        We, or any selling stockholder, may designate agents who agree to use their reasonable efforts to solicit purchases of shares of our common stock described in this prospectus throughfor the underwriters named below. Bear, Stearns & Co. Inc. and UBS Securities LLC are the representativesperiod of the underwriters and the joint book-runners of this offering. We have entered into an underwriting agreement with the underwriters. Subjecttheir appointment or to the terms and conditions of the underwriting agreement, each of the underwriters has severally agreed to purchase the number of shares ofsell our common stock listed next to its name in the following table:on a continuing basis.

        The underwriting agreement provides that the underwriters must buy all of the shares if they buy any of them. However, the underwriters are not required to take or pay for the shares covered by the underwriters' over-allotment option described below.

        Our common stock and the common stock to be sold by the selling stockholders are offered subject to a number of conditions, including:

•

receipt and acceptance of our common stock, by the underwriters; and



•

underwriters will acquire the underwriters' right to reject ordersshares for their own account. The underwriters may resell the shares in wholeone or in part.

        In connection with thismore transactions, including negotiated transactions, at a fixed public offering certainprice or at varying prices determined at the time of sale. The obligations of the underwriters to purchase the shares will be subject to the conditions set forth in the applicable underwriting agreement. Subject to such conditions, the underwriters will be obligated to purchase all the shares offered if they purchase any of such shares. The underwriters may change from time to time any initial public offering price and any discounts or securities dealersconcessions allowed or reallowed or paid to dealers. We may distribute prospectuses electronically.use underwriters with whom we have a material relationship. We will describe the nature of any such relationship in any prospectus supplement naming any such underwriter.

Over-Allotment OptionDirect Sales

        We, or any selling stockholder, may also sell shares directly to one or more purchasers without using underwriters or agents.