- The original home video release replaced the theatrical end credit roll (the credits rolled over an image of the last shot of the film) with a different, video-based one (end credits rolling over an image of Aughra's face.). Subsequent home video releases restored the original end credit roll.
- The 5.1 audio track created for the 25th Anniversary DVD and subsequent Blu-ray contains some additional dialogue and other audio differences not present in any previous video version, nor in theatrical prints.
- When Jen is at Aughra's, trying to decide between the three shards, his voiceover now includes the line "I know," just before he pulls out his pipe.
- After the Scientist's line "Oh it will make you young again sire," he goes on to say, "...and as Emperor you deserve it."
- When the second landstrider is attacked by the Garthim, Kira is heard yelling, "NO!"
- When the General orders the Chamberlain's robes returned, the Chamberlain's whimper is a different take than in the original mix.
- As Kira calls the animals to freedom in the laboratory, the Scientist can be heard shouting, "Back! Back to your cages!"
- Additionally, Jen's gasp when he sees Kira's footprint (just before Fizzgig startles him) is missing.
- When Kira knocks out the Crystal Bat with her slingshot, the sound effect of the actual hit is mixed lower than before.
- Jen's line "Come on!" to his landstrider is almost drowned out by the music, when before it was heard much more clearly.
- On the 1999 DVD, the end credits music contains an odd edit about 40 seconds into the credit scroll. About 25 seconds of music is replaced with a section from later in the cue. This affects both the stereo and 5.1 audio tracks, but on the isolated score track the cue plays out as it does in the theatrical version.
- In the 1994 VHS release, the first five minutes (up to the end of the credits) and the closing credits were in widescreen. Beautiful Celtic-style stone patterns overlapped the top and bottom widescreen bars. The 1994 VHS also removes the Universal Pictures logo.
- The Dolby Atmos remix featured on the 35th Anniversary UHD release removes most of the extra dialogue that was heard in the previous 5.1 remix (though the alternate whimper take when the Chamberlain regains his robes is still there). It also adds further embellishments, such as added reverb on the Mystics' Chord.
- The film originally had the Associated Film Distribution logo preceding the then-current Universal Pictures logo at the beginning during it's original U.S./Canadian theatrical release in 1982. All subsequent home video/TV prints in North America have since deleted the AFD logo entirely and instead go straight into the Universal Pictures logo.
- A Skesis funeral scene for the Emperor was cut from the original release. The negatives from this scene were lost, but a home video of the scene appeared years later on special-edition LDs and DVDs.
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