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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-K

(Mark One)

For the fiscal year ended December 31, 2003

For the transition period from              to             

Commission file number: 000-30267

ORCHID BIOSCIENCES, INC.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (609) 750-2200

Securities registered pursuant to Section 12(b) of the Exchange Act:

None

Securities registered pursuant to Section 12(g) of the Exchange Act:

Common Stock, $.001 Par Value Per Share

Preferred Share Purchase Rights

(Title of Class)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  Yes  x    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  ¨

Indicate by check mark whether the registrant is an accelerated filer (as defined in Exchange Act Rule 12b-2).  ¨  Yes    x  No

The aggregate market value of the registrant’s Common Stock held by non-affiliates of the registrant (without admitting that any person whose shares are not included in such calculation is an affiliate) computed by reference to the price at which the Common Stock was last sold as of the last business day of the Registrant’s most recently completed second fiscal quarter was $73,695,524.

As of March 24, 2004, the registrant had 110,720,232 shares of common stock outstanding.

DOCUMENTS INCORPORATED BY REFERENCE

The following documents (or parts thereof) are incorporated by reference into the following parts of this Form 10-K: Certain information required in Part III of this Annual Report on Form 10-K is incorporated from the Registrant’s Proxy Statement for the Annual Meeting of Stockholders to be held on June 11, 2004.

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ORCHID BIOSCIENCES, INC.

FORM 10-K

INDEX

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PART I

The following Business Section contains forward-looking statements, which involve risks and uncertainties. Actual results could differ materially from those anticipated in these forward-looking statements as a result of certain factors. (See “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Risk Factors”).

Item 1. BUSINESS

We are engaged in the development and delivery of genetic testing, or genotyping, services that generate information related to disease susceptibility and genetic uniqueness, or the genetic variability that distinguishes one organism from another. This information is generated from the analysis of DNA.

DNA based genotyping, or analyzing DNA by identifying a single difference in the nucleotide base of DNA for comparing genetic variability between people, has become a widely used standard technology for the establishment of paternity and forensic identification. Genotyping has also been adapted for food safety and selected animal testing applications (which we refer to as public health testing). Our business includes public health testing services, such as animal susceptibility testing to breed sheep resistant to scrapie disease. Our services are used extensively in each of these applications and we expect their uses to increase. We also expect our services to be used in new genotyping markets, such as food traceability; or being able to identify the source of a meat or plant product based on genotyping.

We conduct paternity genotyping determinations for government agencies and private individuals in North America, and provide forensic DNA testing for primarily government agencies in the United States (US). We also have operations located in the United Kingdom (UK), which provide paternity, forensics and animal susceptibility testing.

Our principal executive offices are located at 4390 US Route One, Princeton, New Jersey, 08540. Our telephone number is (609) 750-2200 and our web site address is www.orchid.com. Our Corporate Code of Conduct and Ethics as well as our Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q and Current Reports on Form 8-K and all amendments to these reports, which have been filed with the Securities and Exchange Commission (SEC), are available to you free of charge through the Investor section on our website as soon as reasonably practicable after such materials have been electronically filed with, or furnished to, the SEC. The public may read and copy any materials we file with the SEC at the SEC’s Public Reference Room, 450 Fifth Street, NW, Washington, D.C. 20549. The public may obtain information on the operation of the Public Reference Room by calling the SEC at 1-800-SEC-0330. Because we file reports and other information with the SEC electronically, the public may obtain access to those documents at the SEC’s Internet web site: http://www.sec.gov. We include our web site address in this Annual Report on Form 10-K as an inactive textual reference only.

History

We incorporated as a Delaware corporation and began operations in 1995. In the first three years of business we were primarily focused on developing our microfluidics technologies for applications in high throughput production of small molecules under collaborative research programs with SmithKline Beecham and Sarnoff Corporation. Microfluidics is primarily the movement and pumping of very minute fluids, which was essential to the mechanization of laboratory research. In 1998, we made a fundamental shift in our business focus to apply our technology to determine genetic variability and differences, including single nucleotide polymorphisms, or SNPs, and perform genotyping services. At this time, we acquired substantially all of the assets of Molecular Tool, Inc. (Molecular Tool), a wholly owned subsidiary of GeneScreen, Inc. (GeneScreen). Molecular Tool’s proprietary primer extension technology, which enabled us to determine a single base pair variation within DNA, for genotyping SNPs matched our existing microfluidics technologies and allowed us to focus our business on genetic diversity. We also developed instruments and kits that could be used for genotyping to be performed independently by third parties. Although we do not currently utilize our microfluidic technology, we do license this technology to others for their use. In December 1999, we acquired GeneScreen, a provider of services to

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determine identity based on genomic technology, or identity genomics. In 2001, we acquired two other identity genomics businesses: Cellmark Diagnostics (Cellmark), a business division of AstraZeneca, a provider of DNA laboratory testing in the UK and a supplier of genotyping products for human inherited disease diagnosis; and Lifecodes Corporation (Lifecodes), a national provider of identity genomics testing for forensics and paternity with multiple laboratories in the US, and a provider of human leukocyte antigens, or HLA, genotyping products and services for transplantation compatibility testing.

In early 2002, we began the process of realigning our business into strategic units for marketing purposes. As a result of this realignment, we organized our business into four business units consisting of Orchid Identity Genomics, Orchid Diagnostics, Orchid GeneShield, and Orchid Life Sciences. Additionally, our international operations, which encompassed all of our business units, were managed under a regional business unit, Orchid Europe. The business units operated in the following areas:

At the end of 2002 and throughout 2003, we sharpened our business focus and moved away from the multiple business units established in early 2002. We concentrated our efforts on genotyping services directed towards forensics, paternity and public health applications, which were the basis of the Orchid Identity Genomics business unit. As part of this strategy, we have discontinued the operations of the Orchid Life Sciences and Orchid Diagnostics business units and have scaled back significantly our pharmacogenomics efforts formerly conducted by the Orchid GeneShield business unit.

After we exited these businesses, we determined that we operate our business under one segment, the development and delivery of genetic testing, services that generate information related to genetic susceptibility and uniqueness, or the genetic variability that distinguishes one organism from another. During the quarters ended March 31, June 30 and September 30 of 2003, we reported Orchid public health as a separate segment, however, upon further analysis, we concluded public health should be included with our Identity Genomics business unit and we now operate under one reporting segment. Financial information relating to such segments can be found in Note 15 to the consolidated financial statements.

Discontinued and Limited Operations

From its inception in 1995, Orchid has engaged in several different technologies and businesses that the company has since elected to exit.

Orchid Diagnostics

In January 2004, we completed the sale of certain assets related to Diagnostic products and services, previously included in our Diagnostics business unit, to Tepnel Life Sciences, plc for a combination of $3.5 million in cash and assumption of certain liabilities, which is subject to a further adjustment in respect of net

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assets once completion accounts have been prepared and agreed by both parties. As part of this transaction, we sold substantially all of our assets and liabilities related to our HLA genotyping services for transplant compatibility matching along with the HLA genotyping products including the Lifematch system, and our ELUCIGENE product line for the diagnosis of mutations associated with inherited diseases including cystic fibrosis in the US and Europe. The transaction included transfer of one of our facilities and all employees associated exclusively with the business unit. In connection with the sale of these assets and liabilities to Tepnel, we were required to sign an unconditional guarantee related to a lease for the Stamford, Connecticut facility, which was assigned to Tepnel. We also reflected the fair value of the guarantee of $1.6 million as a reduction to the net realizable value of these assets and liabilities.

Orchid GeneShield

In May 2003, we realigned our personalized medicine business, to reduce the staff and consolidate operations of the entire business unit, significantly. This was done in response to slower market acceptance of the use of genetic information in personalized medicine. We expect that this leaner and more flexible approach will allow expansion of efforts if and when market forces accelerate or change. We do not currently provide products or services through this business unit but maintain rights to certain intellectual property associated with personalized medicine.

Orchid Life Sciences

In December 2002, we sold certain instrumentation related assets to Beckman Coulter, Inc. (BCI) for a combination of cash payments of $1.1 million and BCI’s assumption of approximately $0.6 million of debt obligations. In connection with this transaction, BCI acquired certain rights to the SNP genotyping instrumentation and related consumables, reagents, and software formerly marketed by our Orchid Life Sciences business unit, as well as other patent and trademark rights. BCI received an exclusive license to use our proprietary primer extension SNP analysis technology in products sold to the research and specialty testing markets, and a non-exclusive license to use our primer extension technology in the field of diagnostics. We also entered into a supply agreement with BCI, which was amended in December 2003 whereby we would continue to purchase certain components necessary to our paternity testing services business. Under the terms of the amended agreement, we committed to purchase a minimum amount of materials and supplies in the amount of $0.6 million during 2003, $0.7 million during 2004, and $1.3 million during 2005 from BCI. These payments are subject to BCI meeting the terms and conditions of the agreement as amended, including manufacturing product to our specifications. We retained rights to use the primer extension technology in all of our genotyping service businesses, including identity testing for forensics and paternity, public health applications, and specialty testing markets including diagnostics and pharmacogenomics.

Background

Newer genetic analysis techniques and technologies are being applied to long-established DNA testing applications, such as identity determination for forensics and paternity. The most common form of genetic variation is that of a single DNA base, called a single nucleotide polymorphism, or SNP. SNPs have become a primary focus of genetic variability studies, and we expect them to become even more important as their impact is better understood. Technology we developed for analyzing SNPs has significant utility in each of our current genotyping testing businesses. The identification of some of the nearly 3,000 victims of the World Trade Center disaster on September 11, 2001 was aided by the use of our SNP technology. Our expertise in deploying these technologies into our established businesses provides ongoing opportunities for improvement in operations and financial performance. As genomic information and genetic variability are better understood, there are increasing demands for the services, which utilize the expanding information base and opportunities to apply this information in useful ways. Our testing services target some of the largest of such applications, where value-added testing is established and exhibiting attractive growth.

Genetic information provides a basis for identification of individuals, as well as an understanding of biological and medical functions in organisms. In recent years, scientists have analyzed large portions of

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deoxyribonucleic acid, or DNA, to determine the sequence of nucleotide bases in the DNA within the human genome and within the genomes of plant and animal species, with the objective of understanding and using this molecular level knowledge to transform traditional approaches to medicine, agriculture and other fields. With the first phase of the human genome sequence completed in 2000, attention has turned from mapping the sequence to identifying genetic differences between individuals to applying this knowledge in healthcare and other related fields where genetic variability is of use. The earliest and most established markets use proven technologies in identity applications, using genetic differences and similarities to identify individuals or infer their genetic relatedness. The increasing availability of genomic data derived from species other than humans is driving the use of genetic variability information for animal identification, to produce improved characteristics in livestock or crops, and to protect against animal-borne diseases. The introduction of DNA testing in the criminal justice system, both in the US and abroad, has been characterized as the most significant improvement in forensic science since the introduction of fingerprinting over one hundred years ago. Not only does DNA evidence afford prosecutors with a means of absolute identification of a defendant by the biological evidence he or she left behind at the crime scene, but DNA evidence has proved to be the best means for a wrongfully accused individual to prove his or her innocence beyond a reasonable doubt. Studies published by the FBI indicate that approximately 30 percent of primary suspects arrested in sexual assault cases are excluded from the suspect pool based on use of this technology. Also, in post-conviction testing of previously untested evidence, there have been in excess of 140 prisoners exonerated to date in the US through the use of DNA testing, including more than a dozen that were death row inmates.

Technologies Utilized

All DNA testing for identity purposes examines specific segments of DNA (also known as markers) that exhibit variability between individuals and animals. Two forms of such variability are known as Short Tandem Repeats (STRs) and SNPs.

STRs

An STR is a portion of DNA in which small segments are repeated a variable number of times. Typically, there might be 10 to 25 possible variations of a given marker, with each person having just one or two variations. By looking at a moderate number of STRs, a DNA profile is determined that is virtually unique for each individual, except in the case of identical twins whose DNA patterns are identical. In the US, there are 13 standard markers that are analyzed by the FBI and throughout the industry to identify felons who are profiled and recorded into a national felon database known as the Combined DNA Index System, or CODIS.

A DNA profile can be determined from any type of biological specimen containing nuclear DNA, including blood or a tissue sample such as a cheek swab. These specimens may be used for paternity testing, for determining profiles of suspects, victims, and felons, and for determining the profile of an animal in both susceptibility and traceability applications as detailed further in the description of public health testing below.

A DNA profile can also be determined from DNA contained in biological evidence from a crime scene, such as blood stains, semen, and even minute samples resident in cigarette butts or postage stamps. DNA profiles from evidence can be compared with that of a suspect or victim, or can be catalogued in a database much like fingerprint data for future comparison. DNA testing can also be used to prove a person’s innocence in a crime and help to exonerate individuals who have been wrongly convicted and imprisoned. In various countries around the world, DNA samples are collected from convicted felons, profiled and entered in a national database. Evidence from crime scenes where there is no suspect can then be analyzed and compared with this database to identify a suspect.

DNA testing may be used in paternity testing. Since DNA markers are inherited, the profile of a child is compared with the mother and alleged father. The alleged father can then either be excluded as the biological father or assessed to be the likely father with a high probability. Similarly, DNA markers can prove familial relationships for individuals immigrating to a country or for children being adopted by foreign nationals.

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SNPs

The second form of variability in DNA involves a change in a single nucleotide base, otherwise known as a SNP. Identifying SNPs can have significant effects on both disease susceptibility and drug response. It is anticipated that each individual has between three and ten million SNPs. By looking at a moderate number of SNPs, between fifty and seventy, a unique genetic profile can also be determined for an individual human, animal or organism. SNPs also have the advantage over STRs of being contained in smaller segments of DNA that are more likely to survive the environmental degradation that can occur due to extreme elements such as water and heat. As such, they may work when STR markers fail to produce a reliable result. It is this characteristic that has prompted the use of SNPs in the process of identifying victims of the World Trade Center disaster.

SNPs can also be used to determine patterns associated with disease susceptibility or resistance, such as the identification of a profile of SNPs in sheep which can be used to determine whether sheep have susceptibility or resistance to the animal disease, scrapie. By identifying sheep that are susceptible to scrapie, the disease can ultimately be bred out of the sheep population.

Continuing Businesses

Based on review of publicly available information regarding contract sizes and competitor activity, supplemented by industry publications and third party market assessment data, we believe we have the largest market share in paternity and forensics testing of any competitor in the US, and we are a recognized provider of such services in Europe. Based on these same sources, we believe these markets are some of the largest existing markets for genetic analysis today compared to smaller markets for providing such services as testing for familial relations for both immigration and adoption purposes. Through our brand Orchid GeneScreen, we conduct paternity genotyping determinations for government agencies and private individuals in North America. Through our brand Orchid Cellmark, we are a recognized private sector provider of forensic DNA testing in the US. Through Orchid Europe, we provide paternity, forensics and animal susceptibility testing under the Cellmark brand. We have six accredited laboratories in the US and UK, which provide high quality genotyping testing services for these businesses.

In each business, a significant amount of our current testing activity is with established contracts with a number of different government agencies. These contracts are usually awarded through a secure bid process and, when awarded, typically have a term from one to three years. These contracts provide a large base of revenue and testing volume that assists us in capacity and production planning, as well as process optimization. We believe that our experience as a reliable provider of services to government agencies is a valued credential that can be used in securing both new contracts and renewing existing contracts. In each business, we have also identified opportunities for further growth, including new contracts and new private DNA testing service markets as described further below.

After our strategic realignment completed in 2003, we now focus on providing genotyping services in three distinct markets: forensics, paternity and public health.

Paternity Testing Services

We offer paternity DNA testing services to both governmental agencies and private customers. Laboratory testing is done in three accredited laboratories located in East Lansing, Michigan, and Dayton, Ohio in the US and in Abingdon, UK. We have the ability to increase testing volume and therefore grow revenue within the existing facilities and without purchasing additional equipment. In addition, because we use industry standard reagents and instrumentation that have been fully validated, we can add additional processing capacity to meet increased demand at minimal expense. While the reagents and instruments are highly specialized, similar reagent kits and instruments are available from other suppliers, so that in the event our current suppliers were to have a major supply problem, we have the ability to switch to alternative suppliers if needed, at little or no additional cost.

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Government paternity testing

The government, or public, paternity testing market in the US, which comprises the majority of our paternity testing services, involves tests ordered by state or county governmental agencies commonly referred to as Child Support Enforcement Agencies (CSEAs). CSEAs are required by law to identify the biological father of a child in circumstances where a mother applies for public monetary assistance, in order to compel the father to make child support payments or to recoup any disbursements made for the benefit of the child. In the US, the Federal government reimburses 90% of the costs of paternity testing incurred by CSEAs, provided the CSEAs abide by certain Federal regulations. These regulations provide incentives to the CSEAs to increase effectiveness and efficiency in their paternity establishment measures. This has resulted in continued expansion of this market. Services are provided to these agencies under contracts awarded in a competitive bid process and typically have a term of one to three years. The contract bidding process is highly competitive and the criteria used to determine the awards vary. Typically, specifications are issued in the form of a Request For Proposal (RFP) and vendors respond in a sealed bid response by a specified response date. In some cases contracts are awarded solely on the basis of price, while others use a scoring matrix to achieve the desired mix of price, quality and service. In addition to CSEAs, we also provide testing services to US and certain foreign government agencies in charge of immigration. Such testing is done to verify claimed family relationships for visa applications. We provide this testing under contract or from an approved vendor list.

Private paternity testing

Our DNA paternity testing services provided through Orchid Europe are done so strictly on a private basis to individuals, solicitors and health care professionals. We do not perform services or receive revenue for DNA paternity testing services in the UK under any government contracts. Conversely, in the US, due to changing demographics related to out-of-wedlock births, reduced stigmas associated with paternity testing, and increased public understanding of paternity testing, demand for private paternity testing in the US has increased in recent years. During 2002, we began marketing paternity testing services in the private market on a much broader scale, and based on growth achieved during 2003 and continued demand, we expect to aggressively pursue a larger share of the private paternity market. In addition to offering services directly to individuals, in 2003 we began establishing relationships with firms or individuals acting as our marketing agents. Under the terms of these relationships, we supply products and materials to such agents and in return, the agent agrees to exclusively utilize our services for their customers seeking private paternity testing. We are further increasing our marketing efforts to the private sector to increase awareness of our services, increase the number of referral sources and improve our service offerings. These marketing efforts include internet marketing channels, offering innovative sample collection methods, and offering these services to our customers.

We intend to continue to develop and evaluate new technologies for enhancing our laboratory processes, including instrumentation, automation and new testing methodologies, which we expect will provide us with a competitively low cost of operation.

Forensic Testing Services

In the forensic DNA testing business, our laboratory services are performed in four accredited facilities located in Germantown, Maryland, Nashville, Tennessee, and Dallas, Texas in the US and in Abingdon, UK. We have selectively focused certain services in specific facilities, where appropriate, to maximize economies of scale, while at the same time enabling significant capacity for expansion across all facilities in the areas of both suspect and no-suspect casework. The use of forensic DNA testing has enabled law enforcement agencies worldwide to utilize national databases for the identification of suspected perpetrators of crimes in which there are no other leads to identify a criminal. In the US, the CODIS database currently stores the DNA profiles of more than one million convicted felons. When evidence from an otherwise unsolvable crime is DNA tested and the DNA profile from the biological evidence is compared successfully to one of the profiles in the national CODIS database, a match may be generated, revealing the identity of the criminal from the database. To date, more than 20,000 criminal investigations have been aided by matching DNA from evidence against the database.

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We expect the use of this technology will accelerate as law enforcement investigators use this technology to successfully identify criminals in cases where there was previously no suspect. We also anticipate growth in this casework based on legislation both in the US and the UK, increased Federal funding in the US and improved utility of the growing National databases. In the US, there has been a significant increase in the number of contracts to address the backlog of cases with no known suspect for screening against the CODIS database.

We offer forensic DNA testing through Orchid Cellmark, a respected forensic DNA testing provider and is known for its high quality and expert staff, having tested numerous high profile forensic cases drawing extensive media coverage. We test a variety of forensic evidence samples collected at crime scenes and provide DNA identification profiles on individual felons for inclusion in national and state DNA databases. Testing services on criminal casework may be provided to implicate or exclude a known suspect, or may be provided in the absence of a suspect to generate a DNA profile of a perpetrator for searching DNA databases. Although the majority of testing is done for criminal justice agencies, we also provide testing services for defense attorneys as well. Casework testing for government agencies may be provided on an individual case basis or under long-term contract. Contract services are usually awarded through a competitive bid process in which specifications are issued in the form of a RFP and vendors respond in a sealed bid response by a specified response date. Such contracts typically have a term of one to three years. In addition to casework, we also provide felon database testing under contract. DNA specimens are collected from incarcerated individuals according to state laws in the US and national legislation in the UK, and tested by our laboratories to provide a DNA identification profile for inclusion in a national database in either the US or UK. In the US, this database is known as CODIS, and in the UK, the database is known as the National DNA Database^®, or NDNADB. Biological evidence from criminal cases with no known suspects may then be screened against these databases to identify a possible suspect. Databasing contracts are also usually awarded in a competitive bid process similar to that of our paternity testing business and typically have a term of one to three years.

All three of our forensic testing facilities in the US have received the prestigious American Society of Crime Lab Directors-LAB accreditation, a designation that only a small number of non-government DNA laboratories have been awarded. Only five other private forensics labs in the US have earned this respected ASCLD accreditation. The value of genotyping in solving crimes is increasingly being recognized and we anticipate that Federal and state governments in the US and national and local governments in the UK will allocate greater resources to support wider use of DNA. This is evidenced by legislation originally considered by the US Senate and House of Representatives known as “The Debbie Smith Act”, and now encompassed in the President’s DNA Initiative in which the US government indicated its intent to allocate $900 million over fiscal years 2005 to 2009 towards reducing the backlog of forensic testing that currently exists in the criminal justice system. Through a process directed by the National Institute of Justice (NIJ) states may apply for Federal funds to assist in testing the enormous backlog of untested cases with no known suspect. A substantial portion of the awarded funds are designated for outsourcing to private sector laboratories. Contracts are then awarded by the states receiving the Federal funds under competitive procurement. Such contracts are awarded on a matrix of criteria including experience, capacity, quality and price, and are usually for one year with the ability to extend under certain circumstances. Virtually all contracts require either ASCLD or NFSTC accreditation, and our three accredited facilities are actively pursuing these contracts.

On July 15, 2002, we entered into a five-year agreement with Forensic Alliance Ltd. (FAL) to provide forensic testing services as an exclusive subcontractor to all customers of FAL, which include a majority of the police departments in the UK. The agreement may be terminated at each anniversary of the date of the agreement upon twelve months notice by FAL. While this agreement does not guarantee annual minimum service levels or revenue, our provision of services to police departments throughout the UK under this agreement constituted 18% of revenue for the fiscal year ended December 31, 2003.

Orchid Europe is the largest independent supplier of scene-of-crime DNA analysis to UK police forces, providing a full range of forensic DNA services from the routine analysis of DNA samples for submission to the National DNA Database^® to the analysis of evidence for the most serious crimes. UK Government funding for DNA analysis has increased significantly in recent years through its DNA Expansion Plan. Working with FAL,

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Orchid Europe is increasing its forensic DNA business by focusing on quality while driving down processing time. Orchid Europe expects to further expand its casework business by pursuing additional contracts with other police agencies through our partner, FAL.

Each of our forensics DNA testing facilities has broad capabilities in handling the complex evidence samples related to casework. Further, we have developed processes and procedures that allow us to scale up to handle the larger volumes associated with specific contracts, particularly in response to the expanding initiatives to reduce the backlog of no-suspect cases. We started to introduce additional automation processes and new technologies to reduce the labor-intensive aspects of testing. We have also made significant upgrades to our laboratory information system to handle higher complexity operations and volume. We have similarly introduced automation and new technology into our felon data basing processes.

We have continued to expand our service offerings with new technology for special cases and new services such as our DNA Express Service, which provides accelerated testing services at a premium price. Specialty testing services include Y chromosome STR analysis, which is important in sexual assault analysis, as well as mitochondrial DNA testing and SNP based testing, both of which are used on very small or extremely degraded samples. For example, in 2002, we were awarded a multi-year contract by the Office of the Chief Medical Examiner of New York City to apply our SNP technology to analyze DNA samples collected from the World Trade Center disaster site for victim identification. In a pilot program conducted with New York City officials in early 2002, we demonstrated that panels of SNPs could enable the identification of additional victims from DNA specimens that have failed previous attempts with traditional forensic analysis methods. As a part of that pilot program, we have analyzed nearly 15,000 samples related to the World Trade Center disaster and continue to work with the Chief Medical Examiner on remains identification. We anticipate offering this technology upon individual customer request in a commercial format for use on highly degraded forensic evidence.

Public Health Testing

Through Orchid Europe, we currently conduct the major portion of the UK Government’s project to help British farmers breed sheep with reduced susceptibility to the animal disease, scrapie. Following a competitive bid process, we were awarded a multi-year contract in 2001 to generate several million scrapie genotypes per year for the project. The project is part of the innovative National Scrapie Plan, or NSP, for Great Britain developed by the Department for Environment, Food and Rural Affairs, or DEFRA, in conjunction with the Agriculture and Rural Affairs Departments in Scotland and Wales. Scrapie, one of the transmissible spongiform encephalopathies, is an untreatable, fatal disease that affects sheep worldwide. With an estimated UK sheep population of over forty million, scrapie has the potential to cause significant economic losses to farmers. Prevention of the disease agent’s ability to maintain itself is viewed as the most effective way to limit the spread of the disease. As SNPs affect an individual sheep’s susceptibility to scrapie, sheep with SNPs associated with a genetic resistance to scrapie are selected as breeding stock. Over time, farmers expect to produce flocks with greatly reduced vulnerability to the condition and, in turn, decrease the risk of animal diseases disseminating into the food supply.

Scrapie eradication is now expanding into the European Economic Community (EEC) as EEC mandated programs are defined. In February 2003, the EEC passed legislation that sets requirements for genotyping-based breeding programs for scrapie resistance in sheep on a voluntary basis beginning January 1, 2004 and on a compulsory basis beginning April 1, 2005. We expect our success in the UK will result in new market opportunities for us in the European Union.

On August 8, 2001, we entered into a three-year agreement with DEFRA to provide genotyping services on sheep in order to determine their susceptibility to the disease, scrapie. DEFRA is providing this service free of charge to sheep farmers as part of the National Scrapie Plan in order to help farmers breed sheep that are not susceptible to this disease, which is similar to mad-cow disease. This agreement is renewable for an additional two years. Under the agreement, we are guaranteed an annual minimum number of samples to be genotyped at a

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per genotype rate based on a sliding scale, dependent upon volume. Based upon volumes performed during 2003, revenue received under this agreement constituted 13% of revenue for the fiscal year ended December 31, 2003.

The recent outbreak of mad cow disease in the US and worldwide awareness of its effect has expanded interest in food safety, and led to the opening of a new market opportunity using DNA testing for meat traceability for the food industry. By way of example, we recently announced participation in a joint project with Maple Leaf Foods of Canada and Pyxis Genomics to be the exclusive provider of assay development and service testing for Maple Leaf’s pork traceability project. This project will entail development and testing on a panel of markers that enable identification of packaged meat back to the farm of origin.

We currently provide animal testing solely from our facility in the UK. We currently have the necessary capacity to accommodate increased volume within the existing laboratory space and equipment configuration in our UK facility. In addition, because we use industry standard reagents and instrumentation that have been fully validated, we can add processing capacity to meet expansion demands at little or no additional cost.

We continue to develop similar assays utilizing this technology for use on other animals that would either identify susceptibility or determine traceability.

Intellectual Property

Since divesting our non-core and non-profitable businesses, we have adjusted our patent strategy such that we continue to protect existing intellectual property relevant to our focused business of genetic diversity. We rely on both patent and trade secret protection of our intellectual property. However, we cannot be certain that patents will be issued from any of our patent applications or that any issued patents will have sufficient breadth to offer meaningful protection. In addition, our issued patents or patents licensed to us may be successfully challenged, invalidated, circumvented or unenforceable so that our patent rights would not create an effective competitive barrier. The laws of some foreign countries may not protect our proprietary rights to the same extent as US law. Our strategy will continue to concentrate on protection of our intellectual property as it relates to our identity genomic testing service businesses. Our existing patent portfolio continues to reflect our international scope and includes pursuing patent protection mainly in North America and Europe. We currently own, or have exclusive licenses to, 55 US issued patents and 56 foreign patents, and have received a notice of allowance for 1 additional Australian patent application. Additionally, we have 59 pending patent applications of which 11 are US applications and 48 are foreign patent applications. Of our existing patent portfolio, both issued and pending patents, approximately half of the patents are primarily related to microfluidic technology, that is, technology related to moving and pumping very minute amounts of fluids. The remainder of our portfolio is made up of methods to identify SNPs and utilization of SNPs. We have sought and continue to seek patent protection for novel uses of the utility of SNPs in the genetic testing field. In cases where novel uses of SNPs have already been patented by a third party, we may need to obtain a license for the use of this technology to make use of or sell products using such technology. As of December 31, 2003, the majority of our patents have approximately 7 or more years before they expire.

We also own or exclusively license patents covering other areas of our business including paternity, forensic genetic markers and pharmacogenomics, otherwise known as the ability to correlate genetic information and predisposition to disease or adverse drug response. We continue to maintain a number of license agreements that rely on technology we own claimed under US patent numbers 5,888,819, 6,013,431 and 6,004,744. We also provide paternity testing services and public health testing services that rely on the technology claimed in the aforementioned patents, as well technology we exclusively license claimed under patent numbers 5,846,710, 5,856,092. We license these patents under exclusive agreements with Saint Louis University and GeneCo Pty Ltd., Diatech and Queensland University of Technology, respectively.

As part of our efforts to build a technology portfolio for genetic analysis using SNPs, in July 2001 we entered into an agreement with Affymetrix, Inc. whereby we were assigned all right, title and interest to US patent number 5,856,092 as well as all of its counterparts. The original agreement called for payment obligations

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to the original owners of said patent of $1.6 million upon signing and payments as follows: $0.3 million in 2001; $0.8 million in 2002; approximately $1.0 million in 2003; and $1.2 million in 2004. Thereafter, we were obligated to pay annual minimum royalties of approximately $1.2 million in 2005 and increasing to approximately $1.9 million in 2008 and thereafter. In July of 2003, we entered into an amended Patent Assignment and License Agreement with the patent owners, which reduced the purchase obligations to approximately $0.4 million for 2003, and approximately $0.2 million in each of the years 2004, 2005, 2006 and 2007. We no longer have a requirement to pay annual minimum royalties beyond the purchase obligations.

On August 6, 2002, we had entered into a patent assignment agreement with Saint Louis University whereby the University would have assigned us US patent number 5,846,710, upon the University receiving consent from the National Institutes of Health (NIH) to assign such patent. The University informed us in February 2003 that it had not received this consent from the NIH. Effective February 25, 2003 we entered into an Exclusive Patent License Agreement under which we received an exclusive license to the subject patent in all fields and for all uses upon payment to the University of a total of $1.0 million in cash and $0.5 million in common stock. We paid $0.3 million of this cash payment in 2002, approximately $0.5 million in 2003 and the balance will be paid in installments in 2004.

We further attempt to protect our trade secrets by entering into confidentiality agreements with third parties, employees and consultants. Most of our employees and consultants also sign agreements requiring that they assign to us their interests in discoveries, inventions, patents and copyrights arising from their work for us, maintain the confidentiality of our intellectual property, and refrain from unfair competition with us during their employment and for a period of time after their employment with us, which includes solicitation of our employees and customers. We cannot assure you that these agreements will not be breached or invalidated. In addition, we cannot assure you that third parties will not independently discover or invent competing technologies or reverse engineer our trade secrets or other technologies.

We have 39 trademarks for which we have received registrations or notices of allowance in the US and elsewhere. We also have 17 pending trademark applications pending. Some of the key trademarks for which we have either received registrations or notices of allowance include: Lifecodes Corporation, GeneScreen and the Orchid logo.

This Annual Report on Form 10-K contains references to some of our trademarked products and services, for which we have filed registration applications with the US Patent and Trademark Office. All other trademarks or trade names referred to in this annual report are the property of their respective owners.

Government Regulation

The identity testing industry involving both paternity and forensics testing is in general not formally government regulated, but rather establishes and maintains standards and quality through voluntary third party accreditation. The widely recognized body covering paternity testing is the American Association of Blood Banks (AABB), which has accredited our laboratories in Dallas, Texas, Dayton, Ohio, East Lansing, Michigan, Germantown, Maryland, Nashville, Tennessee, and Abingdon, UK. Similarly, for forensic testing, two entities afford accreditation: the American Society of Crime Laboratory Directors (ASCLD) providing laboratory accreditation, and the National Forensic Science Testing Center (NFSTC). Our facilities in Dallas, Texas, Germantown, Maryland, and Nashville, Tennessee have been accredited by both ASCLD and NFSTC. Only eight private forensics labs in the US have earned the respected ASCLD accreditation, three of which are our labs.

In addition to industry accreditations, selected government agencies offer accreditation. The New York State Department of Health has accredited our laboratories in Dallas, Texas, Dayton, Ohio, and East Lansing, Michigan for paternity testing, and our laboratories in Dallas, Texas, and Germantown, Maryland for forensic testing. The Dayton, Ohio facility has been accredited by the Standards Council of Canada (SCC) for paternity testing, which also confers ISO/IEC 17025 accreditation. Our Nashville, Tennessee facility has also been certified under ISO/IEC 17025 standards.

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Genetic diagnostic kits previously sold by us in Europe were classified as IVD medical devices and are covered by the European Directive, 98/79/EC, or the IVDD Directive. The IVDD Directive was implemented into UK legislation in 2000. There was a transition period until December 7, 2003 during which manufacturers had to either comply with the existing national laws or comply with the IVD Regulations and “CE” (the mark of conformity) mark their devices. It is now mandatory for manufacturers to comply with the IVD Regulations. However, given the recent sale of our Diagnostics business, we will no longer be subject to this Directive.

Manufacturers must also comply with the Products of Animal Origin (Import and Export) Regulations 1996 (SI 1996/3124) if it is applicable to their devices. In accordance with these regulations we obtained registration from the Ministry of Agriculture, Fisheries & Food for our UK manufacturing units that export genetic testing kits containing Purified Bovine Serum and Purified Gelatin.

During 2003, we sold a number of IVD products in the UK and have accreditation certificates for our UK quality systems from a Notified Body (SGS Yarsley ICS), having met the requirements of ISO9001, EN46001 and ISO13485. We also received an accreditation certificate meeting the requirements of ISO17025 from the UK Accreditation Service, or UKAS, in relation to our testing laboratory. UKAS is the national body for the accreditation of testing and calibration laboratories, certification and inspection bodies.

In the US and UK, we are also subject to numerous environmental and safety laws and regulations, including those governing the use and disposal of hazardous materials. Any violation of, and the cost of compliance with, these regulations could have an adverse effect on our business and results of operations.

Employees

As of December 31, 2003, we had 403 full time employees and 27 part time employees including forensic scientists, computer scientists, and biologists with experience in the medical diagnostic, genotyping, pharmacogenomic, forensic, animalic, and computer industries. None of our employees are represented by a collective bargaining agreement, nor have we experienced work stoppages. We believe that we maintain good relationships with our employees. Our success will depend in large part on our ability to attract and retain skilled and experienced employees. There can be no assurance that we will be successful in hiring or retaining qualified personnel, and our failure to do so could have a material adverse impact on our business, financial condition and results of operations.

Competition

In each of our markets, we compete with other companies offering services that are similar to those that we offer. Some of our competitors have greater financial, operational, sales and marketing resources, and more experience in research and development and commercialization than we have. Moreover, some competitors may have greater name recognition than we do, and may offer discounts as a competitive tactic.

Our competitors in the field of paternity DNA testing include: DNA Diagnostics, Identigene, Laboratory Corporation of America, Long Beach Genetics, Paternity Testing Corporation and Reliagene in the US, along with DNA BioSciences Laboratory of the Government Chemist Forensic Science, NorthGene, DadCheck, and London BioScience in the UK. In the field of forensics DNA testing, competitors include: Bode Technology Group, Commonwealth Biotechnologies, DNAPrint Genomics, Fairfax Identity Laboratories, Identigene, Laboratory Corporation of America, Myriad Genetics, and Reliagene in the US, along with Forensic Science Service and Laboratory of the Government Chemist in the UK. In animal susceptibility testing, we compete with the Laboratory of the Government Chemist in the UK and GAG Bioscience in Germany.

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Item 2. PROPERTIES

We lease three facilities, which provide us with approximately 62,000 square feet for our operations in Princeton, New Jersey, which serve as our corporate headquarters. We are currently attempting to sublease all or a portion of our current Princeton based facilities. Our corporate headquarters would be relocated to smaller space in the Princeton area should all current space be subleased. We lease an approximately 22,000 square foot facility in Dallas, Texas; an approximately 21,000 square foot facility in Dayton, Ohio; and an approximately 5,100 square foot facility in Sacramento, California. The Sacramento facility was closed in October 2003 and we are currently negotiating an early lease termination. We assigned our lease for an approximately 37,000 square foot facility in Stamford, Connecticut, to Tepnel Life Sciences, plc in connection with the sale of the Diagnostics business unit as of January 21, 2004. In connection with this assignment, we unconditionally guaranteed Tepnel’s obligations under the lease. We also lease an approximately 18,000 square foot facility in Germantown, Maryland, an approximately 18,000 square foot facility in Nashville, Tennessee, and an approximately 9,000 square foot facility in East Lansing, Michigan. In addition, we lease a total of approximately 35,000 square feet in three buildings located in Abingdon, UK for the operations of Orchid Europe. We currently believe our facilities are sufficient to meet our space requirements through the year 2004.

Item 3. LEGAL PROCEEDINGS

On or about November 21, 2001, a complaint was filed in the United States District Court for the Southern District of New York naming Orchid as defendant, along with certain of its officers and underwriters. An amended complaint was filed on April 19, 2002. The complaint, as amended, purportedly was filed on behalf of persons purchasing Orchid’s stock between May 4, 2000 and December 6, 2000, and alleges violations of Sections 11, 12(a)(2) and 15 of the Securities Act of 1933, as amended, and Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated there under. The amended complaint alleges that, in connection with Orchid’s May 5, 2000 initial public offering, the defendants failed to disclose additional and excessive commissions purportedly solicited by and paid to the underwriter defendants in exchange for allocating shares of Orchid’s stock to preferred customers and alleged agreements among the underwriter defendants and preferred customers tying the allocation of IPO shares to agreements to make additional aftermarket purchases at pre-determined prices. Plaintiffs claim that the failure to disclose these alleged arrangements made Orchid’s registration statement on Form S-1 filed with the Commission in May 2000 and the prospectus, a part of the registration statement, materially false and misleading. Plaintiffs seek unspecified damages. Orchid believes that the allegations are without merit and has, and intends to continue to, vigorously defend against Plaintiffs’ claims. In this regard, on or about July 15, 2002, Orchid filed a motion to dismiss all of the claims against it and its officers. Though the court heard oral argument on the motion on November 1, 2002, a decision has not yet been rendered. On October 9, 2002, the court dismissed without prejudice only Orchid’s individual officers, Dale R. Pfost and Donald R. Marvin, from the litigation in exchange for Orchid entering into a tolling agreement with Plaintiffs’ executive committee. On February 19, 2003, Orchid received notice of the court’s decision to dismiss the Section 10(b) claims against Orchid. Plaintiffs and the defendant issuers have agreed in principal on a settlement that, upon a one-time surety payment by the defendant issuers’ insurers, would release the defendant issuers and their individual officers and directors from claims and any future payments or out-of-pocket costs. Defendants await the court’s approval of the settlement documents.

Prior to Orchid’s acquisition of Lifecodes Corporation in December 2001, Lifecodes Corporation sold Medical Molecular Diagnostics GmbH, (MMD), a wholly owned subsidiary of Lifecodes Corporation based in Dresden, Germany to Deutsche Knochenmarkspenderdatei gemeinnutzige Gesellschaft mbH (DKMS), pursuant to a Stock Purchase Agreement dated November 15, 2002 (the SPA). Upon the acquisition of Lifecodes Corporation, Orchid assumed Lifecodes Corporation’s obligations to DKMS under the SPA. On September 19, 2003, Orchid received a complaint filed in the 9th Chamber for Trade Affairs in Cologne, Germany on behalf of DKMS through a Request for Service Abroad of Judicial Documents. The complaint seeks damages under the SPA for DKMS’s cost to acquire MMD. DKMS claims defects in the equipment of the MMD laboratory. Orchid has not reserved any amount related to this case and believes that the allegations are without merit and intends to vigorously defend against these anticipated claims. In addition, in December 2002, Orchid filed a claim in the 29th Chamber for Trade Affairs in Tubingen, Germany against DKMS for significant unpaid accounts receivables that accrued during the

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year ended December 31, 2002. The accounts receivables were for HLA typing services conducted by the Diagnostics business unit, which Orchid sold to Tepnel Life Sciences plc in January 2004. The services performed by Orchid’s Diagnostic business unit were exclusively upon DKMS’ request.

Orchid is a defendant in litigation pending in the Southern District of New York entitled Enzo Biochem, Inc. et al. v. Amersham PLC, et al. The case was filed in October, 2002 and is in the early phases of discovery. By their complaint, Plaintiffs allege that certain defendants (i) breached their distributorship agreements by selling certain products for commercial development (which they allege was not authorized), (ii) infringed Plaintiffs’ patents through the sale and use of certain products, and (iii) are liable for fraud, unfair competition and tortious interference with contractual relations. Orchid did not have a contractual relationship with Plaintiffs, but is alleged to have purchased the product at issue from one of the other defendants. Orchid has sold the business unit, which is allegedly engaged in the unlawful conduct. As a result, there is no relevant injunctive relief to be sought from Orchid. The complaint seeks damages in an undisclosed amount.

Item 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

No matters were submitted during the fourth quarter of the year ended December 31, 2003.

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PART II

Market Information

Our common stock began trading on The Nasdaq National Market on May 5, 2000 under the symbol “ORCH”. The following table sets forth, for the periods indicated, the high and low sales prices for our common stock, as reported by Nasdaq, for the last two fiscal years:

On March 24, 2004, the last sale price of the common stock was $ 1.85.

Stockholders

As of March 24, 2004, there were approximately 670 stockholders of record of the 110,720,232 outstanding shares of common stock. On February 27, 2004 our stockholders approved a reverse stock split and on March 25, 2004, our board of directors approved the implementation of a 1-for-5 reverse stock split. We expect the reverse stock split will be effective as of March 30, 2004 and our common stock will begin trading on a split-adjusted basis when trading opens on March 31, 2004. Based on the number of shares of common stock outstanding as of March 24, 2004 we expect we will have approximately 22.1 million outstanding shares of common stock after the reverse stock split.

Dividends

During the twelve months ended December 31, 2003, we issued an aggregate of 26,053,237 shares of our common stock in connection with the conversion of 1,172 shares of our Series A convertible preferred stock. In connection with this conversion of our shares of Series A convertible preferred stock, we issued 126,183 shares of our common stock as payment of accrued dividends on the converted shares of Series A convertible preferred stock.

No underwriters were involved in the foregoing offers and sales of securities. The issuance of the shares of common stock issued as a dividend on the shares of Series A convertible preferred stock were made in reliance upon an exemption from the registration provisions of the Securities Act of 1933, as amended (the Securities Act), set forth in Section 4(2) thereof relative to sales by an issuer not involving any public offering and the rules and regulations thereunder. The issuance the shares of common stock issued upon conversion of the shares of Series A convertible preferred stock were made in reliance upon an exemption from the registration provisions of the Securities Act, set forth in Section 3(a)(9) thereof relative to the exchange of securities with no additional consideration and the rules and regulations thereunder. All of the foregoing securities are deemed restricted securities for purposes of the Securities Act. However, the shares of common stock are covered by a resale registration statement on From S-3 filed with the Securities and Exchange Commission on May 30, 2003.

We have not paid dividends to our common stockholders since our inception and do not plan to pay cash dividends in the foreseeable future, as we currently intend to retain earnings, if any, to finance our growth.

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Item 6. SELECTED FINANCIAL DATA