- A common misconception is that only the gold version of the cartridge represented the first version of the game. In reality, a limited number of Version 1.0 gray cartridges were produced following the gold version preorders, before various elements of the game were tweaked, such as the Fire Temple music and Ganon's blood color.
- The original version of the game was released on the Nintendo 64 in 1998. Both a normal gray cartridge and a special golden one were released (as it was not uncommon to release the classic Zelda games in a special edition gold cartridge.) Later re-releases of the game (including the Player's Choice reissue) changed lots of blood in the game from red to green, and changed the Fire Temple music, as it supposedly resembled a Muslim chant. Many glitches were corrected in later pressings as well.
- Reissued on Gamecube as a limited edition disc with pre-orders of The Wind Waker. This limited edition disc includes the Master Quest of the game, previously only available in Japan, which features different dungeon layouts.
- Also reissued on the Gamecube in a "Collector's Edition" compilation sold with Wal-Mart Gamecube bundles. This disc also featured ports of the original NES Legend of Zelda, The Adventure of Link, and Majora's Mask.
- Reissued as a Wii Virtual Console title. However, due to lack of rumble feature compatibility, the Stone of Agony item is now useless.
- Reissued on the 3DS in 2011. This version of the game drastically improves the graphics, revises the script, and makes several other small tweaks to the gameplay. It also includes a "boss challenge" mode and a "mirrored overworld" version of the Master Quest.
- There were two versions made, the gold case which was for preorder only, and the normal gray one. The only difference is that the gold one contains a glitch where you can have different weapons on Epona.
- In the earlier versions of game, blood can be seen at the final battle and vaguely Islamic-sounding music during the volcano dungeon can be found. These things were changed later on to avoid a Teen rating from the ESRB.
- The "upgraded" version of this game, previously available commercially only in Japan, was released for English audiences in 2003, under the title "The Legend of Zelda: Ocarina of Time - Master Quest," on the newer format of Nintendo's 128-bit system aka GameCube (the original game having been written for N64). Basic story & gameplay remained unchanged, but dungeon levels were reconfigured to make them more difficult. This special release was offered only in conjunction with pre-sale orders of the game as a promotional bonus.
- In the Gamecube version of the game, aside from the changes already made, (i.e. Fire Temple music change, Ganondorf's blood changed to green) the symbols on the blocks, switches and Mirror Shield have also been changed because they represented an Islamic symbol.
- The chanting in the Fire Temple in the original version of the game was a Muslim chant in Arabic that translates to "I bear witness that there is no God but Allah." This was removed because Nintendo did not want to offend Muslims who are quite familiar with the chant.
- In the gold version, toward the end of the game, the color of Ganondorf and Ganon's blood is red as a special bonus to pre-orders. In the basic grey version, the blood was changed to a blue-green color.
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