There are a number of differences between the Genesis and SNES versions of the game:
•Woody's expression shown in the title screen is different between the two versions.
•Upon clearing a level in the Genesis version, Woody has a longer dancing animation.
• Cutscenes in the Genesis version have more still images from the movie than the SNES version.
• A bonus game can be played in the Genesis version if you collect a certain number of stars, which is omitted in the SNES version.
•The Day-Toy-Na level bears a striking resemblance to Outrun, which was also released for the Genesis. However, it is not present in the SNES version of the game.
• The staff credits in the Genesis version showcases the character models that were present in the game, which is ommitted in the SNES version.

The title and ending themes of Toy Story on the Sega Genesis (which are covers of Randy Newman's "Strange Things" and "You've Got a Friend in Me" from the movie respectively) use the Commodore Amiga's MOD sound chip, the only Genesis game to use it. Due to the intensive CPU usage caused by the sound chip player, MOD files are only able to be played on static screens, and the rest of the game uses the GEMS sound driver, the standard practice for Western-developed Genesis games. Because of this, any MOD file can be imported into the title or ending of Toy Story, though the sound player is specialized to the Toy Story music and does not play any other MOD file perfectly.

On the back of the SNES and Genesis versions of the game are two small screenshots from what appears to be an early build of the game. Both boxes feature screenshots of the level "Run Rex, Run!" with different sprites for Woody and Rex, while each box has one unique screenshot of their own from different levels. The differing sprites indicate that these screenshots are not from the build used for in-store demos of the game around its release, and nothing else seems to be known about this earlier build.