For somewhat more than half of its history, the United States got along without a general purpose investigative agency . In 1908, over the objections of some members of Congress, Attorney General Charles Bonaparte, the grandson of the French emperor's brother, issued an executive order creating such an investigative force within the Justice Department.

The agency almost immediately became the subject of intense controversy. With the entry of the United States into World War One, the Bureau of Investigation became engaged in an embarrassing roundup of thousands of young men, only a handful of whom turned out to be genuine draft dodgers. Shortly after the war, the Bureau was the lead agency of an operation that became known as the Palmer Raids — the dragnet arrests of tens of thousands of alien radicals in 33 cities. Partly because most of the victims were arrested without a warrant, the majority were eventually released either before or after their prosecution. One of the supervisors of Palmer Raids was a young Justice Department lawyer named J. Edgar Hoover.

In 1924, following a round of additional scandals and the forced resignation of Attorney General Harry Daughterty, Hoover was selected to clean up the disgraced agency. In 1935, it was renamed the Federal Bureau of Investigation. Hoover would remain the director of the FBI until his death in 1972. During the 1930s, with the help of an aggressive public relations program, the FBI won wide support from the American people for its capture of a handful of highly publicized gangsters. With the coming of World War Two and the Cold War against the Soviet Union, the FBI's reputation as the nation's premier enforcement agency continued to grow.

But with the 1971 theft of internal documents from an FBI office in Media, Pa., and the post-Watergate Congressional investigations in the mid-1970s, the FBI's national reputation plummeted. The documents and the investigations showed that under Hoover's direction the FBI had invested a growing part of its budget and staff for political, rather than enforcement, purposes. The FBI's Counter Intelligence Program — COINTEL — began as an effort to undermine the Communist Party. The Ku Klux Klan, black political activists such as Martin Luther King, student protesters against the Vietnam War and even some early leaders in the women's liberation movement ultimately were added as COINTEL projects.

Following this blackest time in FBI history, well-meaning FBI directors like Clarence Kelley and Judge William Webster worked hard to re-establish the bureau as the nation's leading investigative until In 1993, President Clinton appointed a former FBI agent, federal prosecutor as bureau director. During his term, the efforts of Kelley and Webster were marred by the development of a series of new problems, among them at Waco and Ruby Ridge. Another more systematic problem was serious short comings uncovered in the FBI's National Laboratory. Then came information raising numerous questions about the performance of the FBI in investigating individuals involved in the 9/11 attacks and the espionage conviction of a senior FBI intelligence agent named Robert Hansen.

On September 4, 2001 President Bush name Robert S. Mueller III as the bureau director. Since his appointment, Mueller — a highly respected former U.S. Attorney — has been faced with leading the bureau in the post 9/11 world. Central to this effort has been Mueller's effot to gradually shift the bureau from an agency mostly focused on the criminal prosecution of traditional crimes to an one where a sophisticated kind of counter intelligence is a much larger part of its work.