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 scene when a can is thrown at John Malkovich's head is real. 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.
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.
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.
In a radio interview writer Charlie Kaufman explained that while pitching John Malkovich's representatives the story, Kaufman was informed by them that, much to his surprise, Malkovich lived at the time in a Manhattan apartment numbered 7-1/2. Kaufman said that the representatives gave the impression of "feeling him out" and were worried he was a stalker.
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". John Malkovich himself suggested that Jonze cast Cruise.
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.
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 actors 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.
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.
John Cusack read the script after he had asked his agent to present him with the "craziest, most unproduceable script you can find." Impressed with it, he asked his agent to follow its progress and book him an audition, which won him the role.
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!"
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).
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".
Charlie Sheen was in rehab when he heard about fledgling filmmaker Spike Jonze's eagerness to cast him in this, his feature directorial debut. Sheen accepted the role without initially reading the script.
Cameron Diaz's make-up artist Gucci Westman described styling her in her role as "a challenge, to make her look homely." The script included minimal physical descriptions of characters, and when Diaz took the role she did not know that "people weren't going to recognize me."
Charlie Kaufman wrote the script in 1994, after his time writing for Get a Life (1990). The script got him more work writing for television, but studios didn't know what to do with it. Used to working with a writing partner, Kaufman decided to collaborate with himself, and married two seemingly disparate ideas he had into the same script. One was a man falling for a woman who wasn't his wife, and the other was someone finding a portal into John Malkovich's head. In 1996, Spike Jonze read the script.
John Malkovich claimed that he approached the character of "John Malkovich" as he would any other fictional role, and that the only thing about his real-life that was reflected in the film is his wardrobe.
The original script was much different. Instead of Craig making Malkovich a famous puppeteer, in the original script he announced to the world that he is the master puppeteer and Malkovich is his puppet. He does a one-man show in Las Vegas. Mr. Flemmer (of Mertin-Flemmer) is actually the devil, and tries to convince Craig to get out of Malkovich's mind so that he and his group can take over the world. When Craig and The Great Mantini, the world's best puppeteer, challenge each other, Flemmer controls The Great Mantini's Harry S. Truman puppet, which culminates in Flemmer raising the real Truman from the grave to tell the audience to vote for Mantini. A defeated Craig leaves the vessel, and Flemmer and company take over as Malkovich and have him rule the world. Craig and Lotte reunite, but it's revealed that The Great Mantini is controlling him, and Flemmer is controlling The Great Mantini, and when Flemmer laughs, his throat looks like the tunnel to the vessel that goes into Malkovich.
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.
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.
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.
Lotte can also evoke Charlotte from Johann Wolfgang von Goethe's "The Sorrows of Young Werther", which not only deals with unrequited love but a love triangle. This also became a puppet show Craig-as-Malkovich devised.