Two FBI agents were on the set at all times.
J. Edgar Hoover personally chose James Stewart for the role of Chip Hardesty because he felt that Stewart conveyed a positive image.
J. Edgar Hoover forced director Mervyn LeRoy to reshoot a scene because he didn't approve of one of the extras.
This movie is a favourite of F.B.I. Special Agent Dale Cooper in Twin Peaks (1990). As he states the first time he uses his tape recorder December 25, 1967: "Above my bed on the wall is my most important personal item, a poster of Jimmy Stewart in the movie The FBI Story which only I can touch."
The Jack Graham airliner bombing piece is basically correct, and Graham's real name is used.
J. Edgar Hoover: sitting at his desk in his office during the airline bombing segment. Clyde Tolson walks into the shot.