The new forensic DNA sampling was authorised by the US congress in January 2006 in a minor amendment to a bill that focused on violence against women.
Some civil liberties advocates, however, have called the rule intrusive and overreaching.
Caroline Fredrickson, legislative office director of the American Civil Liberties Union (ACLU), said: "Wholesale DNA collection violates basic American values about our right to privacy.
"DNA is far more than a simple fingerprint.
"DNA testing reveals medical information about individuals and their families – and the practice of keeping these samples permanently is an open invitation to data mining," she said.
"Prosecution of rapists will be further delayed by this poorly conceived program.
"The huge backlog of rape kits waiting to be tested will continue to grow as the government collects DNA from hundreds of thousands or even millions of individuals arrested or detained."
However the law has strong support from organisations that represent victims of crime, and some women's groups, who say it will help law enforcement identify perpetrators of sexual abuse.