- In season 2, episodes "The Web"/"The Net" contain mostly overlapping material but told from a slightly different perspective. But only "The Net" has a definitive conclusion so the US Sci-Fi Channel decided not to show "The Web" at all.
- In the original broadcast of "I worship His Shadow" the scene of when Stanley Tweedle is on its way to the heretics, followed by the ForeShadow, is shown. It was said that this events occur eight years earlier than the main story begins and Thodin gets transported to the Cluster. It was cut in the "second version" of IWHS, nobody knows why. Even though John Dunsworth, who plays the Asteroid commander of the heretics at this scene, is credited, he made no appearance in the "second version".
- In the original broadcast of "I worship His Shadow" the battle between Thodin and Kai was in a cave. In the "second version" of IWHS it was high above the Cluster. Also in the original version, there was no voice-over by Kai before the Brunnen-G anthem appears and BugBomb had no voice.
- Episodes of season 4 which have a more mature adult theme was only shown once in Canada and never repeated again, not even in syndication.
- All episodes (except the third) were slightly cut for German video release. A few minutes were cut from the third episode because it was rated "Not under 18".
- The very end of the US cable/video version of part 4.0 "Giga Shadow" was changed. In every other version except the US, Kai's eyes darken at the end. The UK broadcast version and the German video version of 1.0 "I Worship His Shadow" did not have a voice track for BugBomb (the flying insect from Thodin's nose), which reportedly made his part confusing in those versions. A flashback scene from 4.0 "Giga Shadow", showing Stanley getting captured by Sub-Ns, was used in the UK broadcast version of 1.0 "I Worship His Shadow", while it wasn't in most other versions.
- In most versions, a scene where Stanley and Zev talk while Zev showers is cut.
- The first season of the series originally consisted of several 2-hour movies linked together as a mini-series called "Lexx: The Dark Zone" (1997) (mini).
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