- Although the opening titles claim the film was based on "the diary of the monk Gaspar de Carvajal", no such diary exists - indeed, director Werner Herzog has admitted that there is no historical basis for the story and that the monk's diary was invented to lend it more credence. See also Lektionen in Finsternis (1992).
- According to director Herzog, Klaus Kinski threatened to abandon the film entirely at one point during the shooting. Herzog says he threatened to kill Kinski and then turn the gun on himself if Kinski left - and later declared he was quite prepared to do so. Kinski stated in interviews that Herzog wielded a pistol to emphasize the threat, but Herzog denies this.
- Near the end of the shooting, Herzog thought he had lost all the negatives that Aguirre, The Wrath of God was shot on. He later discovered that the shipping agency at the Lima airport had completed all paperwork that accompanied the transportation of the film cans, but had not actually shipped them. The cans were thought lost for several weeks before the oversight was revealed.
- Most of Aguirre, the Wrath of God, as well as several other features by Herzog, was shot on a 35mm camera that he stole from his film school. He readily admits to the theft but also attempts to justify it with the significance of the films he's made with the camera.
- Many of the scenes depicted in the film were unrehearsed and unstaged, and the dividing line between the cast acting in character and simply reacting to their situations as people became very blurry. For example, in one of the opening scenes, when the carriage holding Aguirre's daughter tips over and threatens to collapse, a hand comes in from the right side of the frame to assist the actors in steadying their hold. That hand belongs to Werner Herzog, the director.
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