In popular perception (or at least in popular media), the Federal Bureau of Investigation chases serial killers, busts countrywide fraud rings, checks out paranormal weirdness, and is generally portrayed as good and law-abiding.

The Central Intelligence Agency, on the other hand, is often perceived and portrayed as an organization of sociopathic American imperialists who like to lie, cheat, steal from foreigners, overthrow governments, and perform unethical psychological experiments.

Expect lots of Interservice Rivalry and Jurisdiction Friction should they run into each other, especially if they are Working the Same Case.

Interestingly, the FBI is very much aware of the perceived moral contrast between themselves and the CIA. FBI agents are taught to be courteous and professional specifically for the purpose of contrasting with the negative CIA stereotype. As a result, there have been cases where CIA informants have requested FBI handlers because of the bureau's reputation.

This has historically been Truth in Television, at least to a degree. J. Edgar Hoover long resented the CIA's existence, as he felt that the FBI should be in charge of the nation's intelligence operations. It didn't help that his long-time rival, William Donovan, headed its precursor, the wartime Office of Strategic Services (OSS). For years under Hoover, the FBI would refuse to share information or cooperate with the CIA in their investigations. Attempts were made over the years (notably by Richard Nixon prior to the Watergate scandal) to ensure smoother relations between the two agencies as their impasse was considered detrimental to national security. Although overt hostility lessened after Hoover's death, interagency tension continued off-and-on for decades. Part of the impetus for the creation of the Department of Homeland Security after the 9/11 terror attacks was that the "intelligence wall" between FBI and CIA was blamed, in large part, for the failure to stop the attacks.

There is some overlap, however, with the abuses of the longtime FBI head J. Edgar Hoover being exposed. The reports of him blackmailing politicians, persecuting political dissidents like Martin Luther King Jr., falsely claiming Ma Barker was a crime boss to excuse killing her in the crossfire of a shootout with the Barker Gang, ruining the lives of competent agents like Melvin Purvis so he could claim all the credit of their work for himself, as well as allegations such as being blackmailed by the mob for being a transvestite, have done much to blacken the name of the FBI under his tenure. Now, the image of the FBI is about stressing how much they have moved beyond the legacy of that hypocritical bully… something not helped by the fact that their headquarters still bears Hoover's name.

It's worth noting that this kind of public perception is almost completely an American phenomenon, without equivalents in other countries, due to the FBI's unusual role as both a day-to-day police force and a semi-covert counter-espionage and state security organisation. For example, both the FSB (successor to the infamous KGB), the internal intelligence agency and the SVR, the external intelligence agency of Russia both suffer a poor reputation amongst Russian citizens due to corruption and political suppression. The FBI's day-to-day law enforcement role is doubly useful for the FBI's reputation because Americans have long tended toward reverence for police.

Compare Sinister Spy Agency, most notably the fact that the National Security Agency (NSA) has been increasingly portrayed in fiction (as of the 21st century) as engaging in the same kind of dirty operations as the CIA, or even being a full-fledged State Sec of the United States, staffed exclusively by Obstructive Bureaucrats. This is likely a result of the agency's notorious secrecy. As the agency responsible for signals intelligence (SIGINT), i.e., intercepting and decrypting the communications of rival and hostile groups, they would not engage in CIA-style fieldwork. (Although they could and have engage in other naughty business.)

Subtrope of Good Policing, Evil Policing.