The home video version cuts one scene from the TV mini series: After Lady Jaye asks Sparks to put a tracer on Cobra Commander's speech and Clutch says "yeah, all you need is a garbage detector", there is a quick shot of Gung-Ho, Cover Girl & Tripwire laughing that has been omitted from the video.
The home video version cuts a second scene from the TV mini-series: After Torpedo blows up the whirlpool and G.I. Joe and Cobra land on the island, there is a short scene where the Baroness tries to raise Zartan on the radio, demanding that he acknowledge her transmission. Zartan replies that he will acknolwedge her when it suits him, and not before. The scene (and video) then cuts to the Guard Statue in the Palace of Doom coming to life.
The Rhino DVD release restores the deleted scenes.
The Region 1 DVD sets from Rhino Home Entertainment feature newly-added sound effects, incomplete/incorrect/missing animation and missing PSAs.