- The American version had several alternative shots during the "All You Need Is Love" song, among others: the population of Pepperland moves in at the Blue Meanies; Paul McCartney doing a somersault, a brief scene of Old Fred and the Mayor dancing together happily. The UK version featured alternate footage, like George floating down from Sgt Pepper's head, saying "It's all in the mind, you know".
- The film originally concluded with the words "Released through United Artists" on the bottom-right-hand-corner of the screen. The 1999 release concluded with restoration credits, the Apple Films logo, and the closing United Artists logo. Current video releases remove all UA references, and only the Apple Films logo appears.
- The UK version contained one extra song, "Hey, Bulldog!", deleted from non-UK prints. This version was re-released to theatres worldwide in 1999 in a digitally restored print with a re-worked soundtrack, plus the "Hey, Bulldog!" number in its original context. This scene replaces the "Beatles to Battle" scene in the International version where the Blue Meanies are defeated by Pepperland inhabitants.
- The British release of the movie had a different ending to the American (and subsequent video) release. Apart from different individual scenes, the American ending has a softer and more considerate feel to it, due to the final conversion of the Chief Blue Meanie to Love, Peace and Music; the British version contains no such sentiments.
- The International (non-UK) of the movie has a sequence with the song "Baby You're a Rich Man" where the Beatles and their Sgt. Peppers look-alikes are dancing after being released from the "glass ball". The UK version initially didn't contain this song. It was added during the 5.1 multichannel mix in the 1998 restoration of the UK version. The original audio version without this song can be heard on the mono track.
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