There are over 20 specialized federal law enforcement agencies, most of which are in the Departments of Justice and Treasury. The most prominent federal law enforcement agencies are the Federal Bureau of Investigation and the Drug Enforcement Administration (in the Department of Justice) and the Bureau of Alcohol, Tobacco and Firearms, the Secret Service and the Customs Service (in the Department of the Treasury). These agencies are located in Washington, D.C., with field offices around the United States, and in some cases, abroad.

Federal prosecutors, called "U.S. attorneys," are appointed by the president for each of 94 judicial districts in the United States. They prosecute only federal crimes in federal courts. As presidential appointees, U.S. attorneys have a great deal of independence, but they are accountable to the U.S. attorney general, who heads the Department of Justice and who is a member of the president's Cabinet.

The Department of Justice's criminal division in Washington, D.C. provides assistance, expertise and some guidance and supervision to U.S. attorneys. The central office of the Department of Justice also includes special prosecutorial units with nationwide authority in such matters as organized crime, war crimes, anti-trust and international drug trafficking; these units usually work in cooperation with U.S. attorneys.

Those federal offenders, who are sentenced to prison, are incarcerated in penal institutions administered by the Federal Bureau of Prisons, an agency within the Department of Justice. These prisons are located throughout the United States; a defendant convicted in federal court may be incarcerated in any federal prison. However, less than 10 percent of all U.S. prisoners are held in federal prisons.