Willem Dafoe could not see for three days, because he got too many eye drops to dilate the pupils of his eyes in bright sunlight to achieve a superhuman effect.
The script for this film sat in the office of Martin Scorsese's lawyer for at least five years prior to being made. Although Scorsese thought the film could be brilliant, he was concerned how the public might respond to the finished film. His lawyer agreed the script was brilliant and very "brave", but advised against making the movie, because he did not think moviegoers were ready for such a story.
Martin Scorsese banned smoking from the set, both because he's a severe asthmatic, and to avoid any photographs being taken of actors and actresses playing Biblical characters, primarily Willem Dafoe, who smoked at the time, with cigarettes hanging out of their mouths.
Universal Pictures agreed to produce the film if Scorsese then did a commercial film. That was Les Nerfs à vif (1991).
Because of the controversy surrounding his role in this movie, Willem Dafoe was refused a role in another historical epic movie, after the sponsors threatened to pull all funding if he was cast. Thus, the role of Doctor John Henry Holliday in Tombstone (1993) went to Val Kilmer instead.
Leo Marks: The voice of Satan was provided by the screenwriter of Le voyeur (1960), a favorite inspiration for Martin Scorsese.
Martin Scorsese: [New York] Most of the apostles with speaking parts were played by actors from the New York City area. Scorsese wanted the apostles to speak with urban New York City accents, because he saw the apostles as "street guys".