In a radio interview writer Charlie Kaufman explained that while pitching John Malkovich the story Kaufman was informed, much to his surprise, that Malkovich lived at the time in a Manhattan apartment located on the 7th 1/2 floor.
John Malkovich was approached about this film several times and loved the script, but he and his production crew felt that another actor would fit the role better. Malkovich offered to help produce the film, and aid Spike Jonze in any way, but refused to star in it. Eventually after a couple of years Malkovich's will was worn down and he agreed to star in the film.
The scene when a can is thrown at John Malkovich's head is real. John Malkovich has described how Spike Jonze wanted to cut it due to running late that night expecting that no one would be able to hit him on the head with a half-full can of beer from a passing car, when about 70 or 80 sets of hands shot up on the crew saying that they would like to try. Eventually the task fell to John Cusack's writing partner and he nailed it on the first try.
Charlie Kaufman sent the screenplay to Francis Ford Coppola after he wrote it. Coppola liked it very much and showed it to his daughter's husband, Spike Jonze. Jonze liked the screenplay so much that he approached Kaufman about directing the movie.
Writer / director Spike Jonze claimed in an interview that when he was shopping the screenplay around Hollywood, at least one unspecified producer asked if he could possibly rewrite the film as "Being Tom Cruise".
Willie Garson (Guy in Restaurant) improvised the scene where he encounters John Malkovich and says, "You were really great in that movie where you play that retard." According to Garson, director Spike Jonze had instructed Garson to use the word "retard" as many times as he could.
Steve Oedekerk was sent an early draft of the script in 1989, and upon reading it, immediately arranged a meeting with Charlie Kaufman. Oedekerk told him he thought it was the most brilliant script he'd ever read, but also that he was certain it could never be made.
In a 2009 Hanes commercial, Charlie Sheen is driving a car with the license plate "MASHEEN". This is reference to the scene in which Malkovich and Charlie Sheen trade affectionate nicknames: Malkovich: "Ma-sheen!"; Charlie: "Malkatraz!"
The play that Craig was performing with his puppets (when he gets smacked by an angry parent) is based on the letters of Abelard and Heloise, written between 1115 and 1117 AD, which were found, copied and abridged by Johannes de Vepria, a 15th century Cistercian monk, into "Ex Epistolis duorum amantium" ("From the Letters of Two Lovers"). This became a classic document of early romantic (tragic) love used by many artists in their work including William Shakespeare in "Romeo and Juliet". In addition, screenwriter Charlie Kaufman's later project Eternal Sunshine of the Spotless Mind (2004) took its title, and no small amount of inspiration, from Alexander Pope's "Eloisa to Abelard".
Several characters in the movie remember John Malkovich as having played a jewel thief, even though, as he correctly points out, he never did. However, Malkovich did eventually play a jewel thief in Johnny English (2003).
In the first draft of the script, Lester and his friends weren't using Malkovich's portal as a means for extending their lives, but in a plot to take over the world in the name of Satan. Satan was the mysterious 'Flemmer' that the Merton-Flemmer building was half named after.
The name of John Cusack's character is a combined reference to Edward Gordon Craig and Bruce Schwartz. Schwartz is an accomplished American puppeteer while Craig was a turn-of-the-century theater artist who suggested that actors should be viewed as no more important than marionettes.
Charlie Kaufman had no "backup actor" in mind to play themselves in the title role if John Malkovich couldn't appear in the film, and every time somebody offered to produce the film on the condition that a different actor be used, Kaufman adamantly refused...even when Malkovich himself made the offer.
The play that Malkovich is reading into a tape recorder is Anton Chekhov's "The Cherry Orchard". The line beginning "I'm as hungry as the winter..." is at the end of Act Two, where Trofimov is speaking to Anya, pontificating on his rejection of materialism.
The play that Malkovich is rehearsing on stage is William Shakespeare's "Richard III". The lines "Was ever a woman in this humour woo'd? / Was ever a woman in this humour won?" are I.ii.239-240, where Richard is gloating over his use of power, lies and crime to obtain the woman he desires, Lady Anne. This rehearsal scene is immediately followed by the first time that Craig has sex with Maxine via Malkovich.
In the scene in the Merton-Flemmer building lobby, when Craig browses the floor listings to find LesterCorp, the camera scrolls past the listing "Eric Zumbrunnen, CPA". Eric Zumbrunnen is the film's editor.