Comparison between the cut Special Edition from the UK and the (also cut) German DVD by Paramount.
The German DVD is 15,5 sec longer than the British one, two scenes were altered.

Running time of the German DVD: 126:50 min
Running time of the British DVD: 126:18 min
The remaining difference in running time is due to different company logos before and after the movie.
Time designations refer to the German DVD. Cuts in the German DVD are not mentioned in this article.

1:36:25
A shot of Indio is missing.
2,5 sec (1 shot)

1:37:47
Indio jumps of the wall and tells his men to stop shackling and guarding the two. One of the guys asks why Indio does not kill them. He answers that there was a time for everything, Groggy then asks what that was supposed to mean.
13 sec (3 shots)