This film contains examples of:
- Acting for Two: John Malkovich plays himself, but also plays Craig, when he's permanently taken over Malkovich's body and assumed his identity.
- And I Must Scream:
- The final fate of Craig, who is forced to watch the life of Malkovich's daughter being raised by the woman he loved and the woman he hated.
- This also happens to Malkovich while Craig was in control of his body for eight months, and this could be his situation for the rest of his life depending on how the whole host thing works.
- Ambiguously Gay / If It's You, It's Okay / Heterosexual Life-Partners: The nature of Lotte and Maxine's relationship by the end of the film is open to interpretation.
- As Himself: See The Danza below.
- Bizarrchitecture: A classic example. I mean, 7 1/2th floor??
- Black Bug Room: Lotte and Maxine run through Malkovich's.
- Brick Joke: When Craig finally leaves John Malkovich's mind forever, he's holding the plank of wood he had at the very beginning.
- California Doubling: The whole movie was shot in L.A., but set in New York. When Lotte falls out onto the New Jersey Turnpike for the second time, look in the background for some palm trees that shouldn't exist.
- The Cameo: Charlie Sheen, Sean Penn and Brad Pitt all play themselves.
- Check Please:Maxine: Tell me a little about yourself.
Craig: Well, I'm a puppeteer...
Maxine: [turns to bartender] Check!
- Downer Ending: And how. Craig jumps into the portal too late. As a result, he is trapped inside the mind of the girl being raised by both of his former wives, unable to affect anything.. Forever. The last lines of the movie are him weeping and pleading that the girl look away from the two women laughing and playing with each other. Given that he turned into a psychopathic Jerkass a certain amount seems like karma.
- Evil Versus Evil: There are no genuinely moral characters in the film, save Malkovich himself, and even he's painted as a bit of a pervert in the trip through his memories. Everyone else is trying to take control of Malkovich, and worse his as yet unborn daughter, with no regard for the fact that they're essentially killing them by suppressing their consciousnesses forever.
- Femme Fatale: Maxine.
- Foreshadowing: Lotte spends the whole first half of the movie making ridiculous, flower-child psychology statements like "Elijah is suffering from some childhood trauma". Then, when Lotte is struggling against the ropes she's tied in, Elijah has a first-person flashback to when his parents were tied up (complete with monkey-language dialogue and English subtitles), and he couldn't untie their bonds before he was captured.
- Craig performs "Craig's Dance of Despair" with a puppet at the opening, then performs it using John Malkovich's body.
- Near the beginning of the movie Craig and Lotte are making dinner and the parrot is being annoying. When Lotte goes to put it up it says "Help! She's locking me in a cage!" and it's kind of cute. Later in the movie however when Craig goes crazy and stuffs Lotte in a cage, she screams "Help! He's locking me in a cage!"
- Early on, Maxine asks Craig, "Are you a fag?" By the end of the movie, she's in a lesbian relationship.
- Craig watches a video where Captain Mertin gets a proposal from a midget in need of help. Later, Lester gets a similar proposal from Lotte (he's even holding the same pipe from the beginning).
- Earlier, Craig is disgusted by a famous puppeteer who is solely a gimmick celebrity. This is ultimately his fate when he controls Malkovich.
- The only thing that Lotte wants from Craig is a child. She finally gets this surprisingly when she becomes a father inside Malkovich.
- Genre-Busting: A comedy drama laden with surrealism which functions as a borderline philosophy course.
- Spike Jonze Script: This movie might wasn't written by Spike Jonze but with him being the director it shows the elements: Most of the main cast act like crazy people yet the world around them is meant to be like the real-life and every person in this movie thinks that our main characters are normal people.
- Grand Theft Me: The entire point of the doorway inside the Mertin Flemmer Building. Turns out that Mertin has been using it for decades to jump from host to host as his current one grows too old... which means that little Emily is doomed to become the next victim.
- Granola Girl: Lotte, and how.
- If I Can't Have You: Lotte to Maxine in the film's climax.
- Karma Houdini: Lester and his friends, Maxine, Lotte... everyone except Craig and Malkovich himself, really.
- Leitmotif: Most of the musical score consists of a single six-chord melody in a canon-like arrangement, making slight adjustments for the given moment or character.
- Loser Protagonist: Craig starts out the movie as a penniless puppeteer. When both he and Lotte try to make a move on Maxine at the same time, she rejects Craig because she doesn't find him physically attractive. Ouch.
- Mainstream Obscurity: An in-universe example. The characters admire John Malkovich immensely, and they seem convinced that he's one of the world's greatest living actors, but none of them can actually name a single movie that he's been in (except "That jewel thief movie", which Malkovich insists he never made).
- Mathematician's Answer:Craig: Hi. Do you know that I don't even know your name, or where you work?
- Malkovich Malkovich: Malkovich Malkovich Malkovich Malkovich, Malkovich Malkovich Malkovich Malkovich Malkovich.Malkovich: Malkovich Malkovich Malkovich?
Malkovich: Malkovich Malkovich.
- Mental Story: A significant chunk of the movie takes place in Malkovich's head.
- Mental World: The chase through John Malkovich's unconscious mind.
- Missing Floor: Level 7 1/2. In order to get there, you have to block the elevator and pry open its door with a crowbar.
- Mind Screw: In more ways than one.
- Pokémon Speak: The Mental World Malkoviches.
- Pop Culture Osmosis: ESPN ran an entire ad campaign on itself using the film's premise, where fans would jump into the bodies of athletes - and end up on the same NJ highway ditch.
- Primal Scene: In Malkovich's subconscious.
- Running Gag: People only knowing John Malkovich for being in "the jewel thief movie", with Malkovich insisting that he wasn't.
- Sex by Proxy: Oh yeah.
- Sitting Sexy on a Piano: Used disturbingly.
- Surreal Horror: A hole in an office buildings that is used to take someone over. The scene where Malkovich tries to go through it.
- Triang Relations: Type 12.
- Unguided Lab Tour: Pretty much how the portal to John Malkovich's psyche is discovered.
- Weirdness Censor: Granted he didn't witness what Malkovich was going through firsthand, but perhaps it's fitting (especially given the events of 2011) that Charlie Sheen didn't think anything Malkovich was saying sounded weird at all. Actually, he found the whole thing kinda hot.
- What Have I Become?: Craig actually says this when he considers how he tied up Lotte and locked her in a cage with her monkey. Then he goes right on doing what he was doing.
- "Where Are They Now?" Epilogue: Of a sort. More like a who are they now epilogue.
Malkovich Malkovich Malkovich. Malkovich.