Alternate versions

The movie was officially restored in 1989 by Kevin Brownlow and David Gill for Thames Television. It was transferred from the best available 35mm materials, color-tinted per D.W. Griffith's intent, and contains a digitally recorded orchestral score by Carl Davis. This 176-minute version was released on video worldwide, but has never been telecast in the U.S.

In addition to the still frames that the Museum of Modern Art utilizes in its restored print, it also uses and discards some footage that did not appear in Kino's video release. Only one scene was reinstated that was comprised entirely of actual moving footage. This scene shows the Dear One taking the Reformers to court over custody of her baby. She becomes infuriated, screaming at them. Her lawyer pleads her case, but it is lost to the Reformers. Some footage seems to have been removed from the Babylonian sequences. There were shots of the dancers and entertainers at the feast and, in an earlier scene, woman frolicking in the temple. These scenes were probably removed because they were shot by Joseph Henabery, separately from D.W. Griffith's production, and would not have been part of Griffith's original vision. Also omitted was one shot from the first scene at court in the French scenes.

According to Kevin Brownlow and John Kobal's book 'Hollywood: The Pioneers,' the version released in Mexico is rearranged so that the four stories play back to back, without any inter-cutting.

Though the Kino DVD is about twenty minutes longer than the Kino VHS tape, the VHS version does contain two scenes missing from the DVD. The first shows the Mountain Girl attacking the treacherous High Priest when he speaks against Belshazzar, which is followed by Belshazzar giving the girl her freedom for the second time. The other is when the Dear One and the Boy are reunited with their baby at the end. In addition, the Kino DVD removes the original 1916 cast and crew credits, which are on the VHS version, and replaces them with DVD production credits.

A print of Intolerance was put together by the Museum of Modern Art in New York, restoring scenes that were excised and that survive only in single badly-damaged still frames. These scenes were:

• In the Jerusalem scenes: more shots of the market with a dove seller that is visible in a long shot that exists in the film; an interlude between the priests and Mary Magdalen; an extension of the wedding ceremony for the bride and groom of Cana.
• In the Babylonian scenes: more shots of the battle scenes and feasting; a scene at the jury where Joseph Henabery has a cameo as an agonized husband. Henabery talked about this scene in Kevin Brownlow's book The Parade's Gone By.
• In the French scenes: a whole subplot in which the assassination of a Huguenot politician (not Coligny) is plotted and carried out (This story is real; the actual events occurred at Blois in 1572.); a street scene that occurs before Brown Eyes and Prosper are introduced - a woman calls out from a window "Look out below!" and dumps the (liquid) contents of a chamber pot into the street below, just as a pedestrian jumps out of the way; a couple more shots of the wedding procession.
• In the Modern scenes: more scenes of the Modern Pharisees doing their evil deeds.

Griffith recut the modern and Babylonian stories and released them as two separate films in an attempt to make up for the financial loss he suffered on the original picture. The re-released versions were The Mother and the Law (1919) and The Fall of Babylon (1919).

The laserdisc contains a scene not featured on the DVD: when the Boy escapes execution and rejoins his wife, the baby is brought back home (which would take the running time to 198 minutes if released on DVD).

The Kino version contains an alternate ending to the "Fall of Babylon" segment where the wounded Mountain Girl falls into the arms of the Rhapsode, and they leave happily to start a new life.