- The Nintendo 64 version, "Duke Nukem 64" removed almost all sexual material. The "Red Light District" level was renamed "Gun Crazy" and Adult stores were changed to gun shops and fast food restaurants.
- When originally submitted for classification in Australia, the game was refused by the OFLC (Office of Film and Literature Classification), which led to the distributors adding code which permanently locked out all gore and sexual references. This was the version which was on Australian shelves in 1996. Later, 3DRealms released a patch which restored the stronger content to the game, allowing players to experience it as originally intended. When the Atomic Edition was released, the game was reclassified, and has ever since been available in its uncensored form.
- The South Korean version is censored; most notably, the blood and gore are re-colored white (only blood puddles and footprints remain red).
- The PC version contains an option entitled Kid Mode. Like Shadow Warrior it removes all the sexual content, language and most of the violence.
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