- In the original conception, three men were seen talking and bathing in red mud. They are startled when Caligula first appears in the hallway outside Tiberius's pool. As Caligula walks down the hall, we see fragments of tortures that occur on the other side of the curtain. In the movie, the scene with the three men was moved *after* Nerva's death, and entirely new dialogue was dubbed over the shot, making it appear that the men are discussing Nerva's recent death and Tiberius's imminent death. They appear to be startled, then there is a cut to Caligula across the palace, fantasizing about torture, intercut with the fragments of tortures that were meant to be about 15 minutes earlier in the film.
- Unused bits from the scene where Chaerea, Longinus, and a few senators discuss the possibility of Caligula dying from a fever were used to build a new scene toward the end of the film where (it appears) the men plot Caligula's murder. Almost all of the dialogue in this scene was invented in the dubbing stages, and most shots obscure the mouths of each speaker.
- The opening is a fragment of a scene that was meant to occur immediately following Tiberius's death (this is why Caligula is clean shaven in this scene, but has a beard in the next). It was supposed to depict Caligula and Drusilla enjoying their new freedom as they no longer need to worry about being seen by Tiberius's informers. The scene is almost certainly shorter than it was intended to be, and thus is now a meaningless fragment.
- The scene that was meant to be the opening is cut in half and moved around. In the final cut, the first half of this scene (which depicts Caligula worrying to Drusilla about Tiberius killing him) occurs between Caligula's tour of the grotto and Nerva's suicide. The second half of the scene (where Caligula and Drusilla fool around and are caught by Macro) now immediately follows the opening credits.
- When Caligula and Nerva walk down the path to Tiberius's pool, we can hear people being tortured behind a curtain, which Caligula looks through at one point. The fragments of people being tortured several scenes later were meant to be intercut with the scene of Caligula and Nerva in the hall. Also, several scenes later, we see bodies being taken off crosses and servants clearing the pathway. These were meant to act as establishing shots for the scene in the hall.
- Mixed in the scene on Tiberius's pleasure grotto are shots of an orgy, some of which filmed through mirrors. It's unclear what the purpose of these shots were, but they were obviously not meant for this scene (as they take place in a different room, and, thus, are cutaways to a location across the palace).
- In the scene where Caligula, Caesonia, and Drusilla have sex, the movie includes inserts of a lesbian tryst that was one of the extra scenes shot by Bob Guccione. This footage replaces shots that made this scene necessary for the plot (the original concept had the palace informers looking through the peephole, thus explaining the closeups of the moon face in the bedroom), as well as a different lesbian act featuring the ladies-in-waiting, shot by Tinto Brass.
- The shot of Caligula being scared by a black bird while playing with a rat was originally part of a much longer scene in which he sets up many small chariots for a race to entertain his daughter, and, thus, was also meant to be included somewhere in between the I am God scene and the imperial bordello scene (along with several other cut scenes (such as the sacrificial scene and the scene where Caligula claims himself to be king of the gods) and relocated scenes (such as Proculus's death)).