- Adaptation.: A meta-adaptation of The Orchid Thief, framed as the story of Kaufman's struggle to script an unfilmable novel adaptation and deal with his evil-hack-writer-twin.
- Being John Malkovich: The feature debut of director Spike Jonze.
- Confessions Of A Dangerous Mind: The directorial debut of George Clooney, although Clooney deviated considerably from the script without Kaufman's permission.
- Eternal Sunshine of the Spotless Mind: Kaufman won the Academy Award for Best Original Screenplay for this film.
- Human Nature: The feature debut of director Michel Gondry.
- Synecdoche, New York: Kaufman's directorial debut about a stage director who creates a life-sized model of New York City in his pursuit of verisimilitude on the stage. Considered by Roger Ebert to be the best movie of the last decade.
- Anomalisa: A Stop Motion animated film based on Kaufman's own play and co-directed by him and Duke Johnson.