Alternate versions

A director's cut prepared by Oliver Stone for the video release features 17 minutes of footage not included in the theatrical version. Among the new material:

• Guy Bannister and his secretary talk briefly about Oswald and laugh.
• New flashbacks of Oswald's life in Dallas with his wife after his return from Russia and his contacts with George De Mohrenshildt, Janet and Bill Williams (the man who gets Oswald a job at the book depository).
• When Garrison and his assistant are at the book depository, they discuss the fact that the motorcade route was changed by then Dallas mayor Earle Cabell, brother of general Charles Cabell fired by Kennedy in 1961.
• A fake Oswald (Frank Whaley) is seen in a flashback test-driving a new car and talking about Russia to the salesman.
• In another flashback, Oswald is introduced to the New Orleans Cuban community and meets Sylvia Odio, leader of an underground anti-Castro movement.
• A new flashback of Oswald and Clay Shaw seen together at a voter's registration drive in September '63.
• Jim Garrison appears on "The Jerry Johnson Show" on TV to be interviewed. He tries to show photographs and defend his theories but he's cut short by host Jerry Johnson (John Larroquette).
• Bill Broussard meets Jim Garrison at the airport where he's leaving for Phoenix, AZ and tells him the mob will attempt to assassinate him. After a few minutes he has to flee from a public restroom when he hears strange voices in the next stall and is approached by an unknown man (a cameo by production designer Victor Kempster) who pretends to be a friend of him.
• Garrison and his staff discover that Broussard has disappeared from his apartment, and argue about the real reason why Clay Shaw has been brought to trial. While they're talking, Garrison sees Robert Kennedy on TV and says "They'll kill him before they'll let him be president".
• During the trial, more witnesses against Shaw are shown than in the theatrical version, including a obviously insane man (Ron Rifkin) who claims that Shaw discussed killing Kennedy with him.

When the film is first released on videocassette (and subsequently on all TV broadcasts as well), an addendum to the epilogue is shown, telling how more JFK sealed records in 1992 were released to the public due to the controversy stirred by the film. It also warns more records have yet to be released.