TWGDAM was sponsored by the FBI Laboratory which hosted several scientific meetings a year at Quantico, Virginia, to accelerate development of laboratory guidelines and peer-reviewed papers to support forensic DNA testing which was, to some, an unproven forensic tool. TWGDAM completed a white paper in October 1989 which provided conceptual and operational concepts for a Combined DNA Index System to share DNA profiles among crime laboratories similarly to automated fingerprint matching which had become commonplace in law enforcement during the 1980s.
In late 1990, the FBI Laboratory began a pilot project with six state and local crime laboratories to develop software to support each laboratory's DNA testing and allow sharing of DNA profiles with other crime laboratories.
The DNA Identification Act of 1994 formally authorized the FBI to operate CODIS and set national standards for forensic DNA testing. The TWGDAM guidelines served as interim standards until recommendations were provided by a DNA Advisory Board required under the Act. Although the Act was passed in 1994, CODIS did not become fully operational until 1998.
CODIS identifies 13 markers, plus AMEL to determine sex:
These markers do not overlap with the ones commonly used for genealogical DNA testing.
In its original form, CODIS consisted of two indexes: the Convicted Offender Index and the Forensic Index. The Convicted Offender Index contains profiles of individuals convicted of crimes. State law governs which specific crimes are eligible for CODIS. (All 50 states have passed DNA legislation authorizing the collection of DNA profiles from convicted offenders for submission to CODIS.) The Forensic Index contains profiles developed from biological material found at crime-scenes.
In the past several years, CODIS has added several other indexes, including: an Arrestee Index, a Missing or Unidentified Persons Index, and a Missing Persons Reference Index.
CODIS has a matching algorithm that searches the various indexes against one another according to strict rules that protect personal privacy. For solving rapes and homicides, CODIS searches the Forensic Index against itself and against the Offender Index. A Forensic to Forensic match provides an investigative lead that connects two or more previously unlinked cases. A Forensic to Offender match actually provides a suspect for an otherwise unsolved case. It is important to note that the CODIS matching algorithm only produces a list of candidate matches. Each candidate match is confirmed or refuted by a Qualified DNA Analyst. (To become Qualified, a DNA Analyst must meet specific education and experience requirements and undergo semi-annual proficiency tests administered by a 3rd party.)
CODIS databases exist at the local, state, and national levels. This tiered architecture allows crime laboratories to control their own data -- each laboratory decides which profiles it will share with the rest of the country. As of 2006, approximately 180 laboratories in all 50 states participate in CODIS. At the national level, the National DNA Index System, or NDIS, is operated by the FBI at an undisclosed location.
The growing public approval of DNA databases has seen the creation and expansion of many states' own DNA databases. California currently maintains the third largest DNA database in the world (naturally, as CODIS contains all states' database information). Political measures such as California Proposition 69 (2004), which increased the scope of the DNA database, have already met with a significant increase in numbers of investigations aided.
In order to decrease the number of irrelevant matches at NDIS, the Convicted Offender Index requires all 13 CODIS STRs to be present for a profile upload. Forensic profiles only require 10 of the STRs to be present for an upload.
Currently, the ACLU is concerned with the increased use of collecting DNA from arrested suspects rather than DNA testing for convicted felons. Along with the ACLU, civil libertarians oppose the use of a DNA database for privacy concerns as well as possible institutionalized discrimination policies in collection.