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All the live action that occurred inside the computer was filmed in black and white, and colorized later with photographic and rotoscopic techniques.
Flynn's program is named "Clu". CLU is an old programming language.
After Flynn escapes from the light cycles arena, it is possible to hear a "Pac-Man" video game and see a graphic on the map he is watching.
In the "solar sailer" sequence, you'll see, for a brief moment, the silhouette of Mickey Mouse on the ground made to look like part of the terrain (most modern Walt Disney movies have hidden Mickey's in them.)
There is a deleted love scene with Tron and Yori in the I/O Tower that never made the final cut.
The light cycle sequence originally had background music. This alternate scene is present on the special laserdisc edition.
The original plan was to have the circuit lines of the "good" programs glow yellow, and the "bad" programs would have blue circuit lines. At one point this was changed to where good programs are blue, and evil ones are red. Some of the original coloring remains, mostly in tank programs (Clu has yellow lines on his uniform, and all of Sark's tank commanders are blue).
Some non-USA versions of the film have a brief prologue of text explaining the difference between the computer world and the real world right before the starting credits.
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