FBI Director J Edgar Hoover outlined the Sex Deviant's Program in two memos sent to various people in the FBI and other federal departments. These memos were the result of significant fears created by a variety of influences, perhaps including Hoover's own personal interest in homosexuals.

The purpose of this program was to build a trackable database of known homosexuals in the United States. Hoover connected the FBI's tracking system with local law enforcement agencies through the collection of fingerprints from those arrested by local law enforcement for any crime related to homosexuality. This could have included "public morals" charges such as holding hands with someone of the same gender in public, dressing in gender inappropriate clothing, or soliciting sex prohibited by law.

"Each Supervisor will be held personally responsible to underline in green pencil the names of individuals mentioned in any report, letter, memorandum, newspaper article or other communication who are alleged to be sex deviates. This will assure proper index­ing by the Records Section."

The special Sex Deviates Program files grew to more than 330,000 pages. It was used to compile and index information to supplement other FBI files in order to disseminate information about gay people to ensure none were employed by the federal government. Eventually, this even included impacting employment in jobs beyond the government, such as local police departments and universities.

Most of these files were incinerated in 1977 and 1978.