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It is important to be specific when referring to the different versions of Ocarina of Time. In keeping with the established Zelda tradition, pre-ordered copies of Ocarina of Time on the Nintendo 64 featured "gold" cartridges. Also, the game's box was made of sturdy plastic instead of cardboard and exhibited the boxed phrase "Collector's Edition." Gold carts were the first American release of Ocarina and were only offered in a limited number, making them collector's items.

The game also released in different software versions. All of the gold cartridge games that came out in November 1998 are version 1.0, and some grey cartridges released soon after are also version 1.0. Version 1.1 grey cartridges began to be released in early 1999, in which Nintendo fixed a number of bugs and glitches from the first version. This was followed by version 1.2.

The most notable difference between version 1.0 and the following versions is that version 1.0 contains a trick that allows one to play the game without Link's sword, which in turn allows one to use any item on Epona. Version 1.1 is similar to version 1.0 except you cannot perform the above trick (there is a different known method that works on all versions, including GameCube ones). Ganon's blood at the end of the game appears red in versions 1.0 and 1.1, but was changed to green in version 1.2. Also for version 1.2, the original theme for the Fire Temple, similar to an Islamic prayer chant, was replaced in version 1.2 with a new theme. The GameCube version is similar to 1.2 but has some differences including button icons changed to their GameCube colors.

In 2002, Ocarina of Time was re-released as a bonus disc on the Nintendo GameCube for those who pre-ordered The Legend of Zelda: The Wind Waker. The bonus disc also included the Ocarina of Time Master Quest, a previously unreleased version of Ocarina of Time with redesigned dungeons and supposedly greater difficulty. Later that year it was again reissued (without the Master Quest add-on) on The Legend of Zelda: Collector's Edition as part of a limited-time promotion. This disc also included The Legend of Zelda: Majora's Mask, The Legend of Zelda and Zelda II: The Adventure of Link. In all the GameCube re-releases Nintendo changed the crescent moon and star symbol of the Gerudo to an original design.

In 2011, the game was remastered as the Legend of Zelda: Ocarina of Time 3D for the Nintendo 3DS. It featured updated graphics, redesigned inventory, a boss challenge mode, and hint movies. It also included the Master Quest, which is unlocked after beating the game. The gyro sensor built into the 3DS can be used to aim for some items. The Stone of Agony was replaced by the Shard of Agony, which chimes and displays an icon in the top left corner of the screen when near secrets.

In 2015, Ocarina of Time was rereleased on the Nintendo eShop. This is a direct port of Ocarina of Time version 1.2, with any changes simply being due to the different hardware it's running on.

Main version difference in consoles[edit]

  • The N64 version (with Majora's Mask) appearance has the usual button settings with the rumble pak.
  • The GC version with Master Quest (and Majora's Mask) has a different colour setting with the rumble feature. Master Quest in particular (available in the GameCube and the 3DS version of the game) has all dungeons redesigned for veterans who find the original too easy or familiar.
  • The Wii version (with Majora's Mask) has the N64 button settings in which you can use the classic and gamecube controls without any access to a rumble pak or feature.
  • The 3DS version, The Legend of Zelda: Ocarina of Time 3D, features remastered graphics, some changes to HUD sprites, ways to use motion sensor controls, touch screen menus, a shortcut to the 3DS Game Notes application, a hint system featuring "Sheikah Stones" (which use videos to give hints and show you what to do, much like in Skyward Sword), The Legend of Zelda: Ocarina of Time 3D Master Quest (unlocked after beating the normal game; it uses the same new features, but this time the game's maps and are mirrored - similar to the Wii and GameCube versions of Twilight Princess or more recently Twilight Princess HD with the Hero Mode), and a "boss challenge" mode that lets you either fight bosses you have beaten before or take on all of them in one continuous battle.
  • The Wii U eShop version features the same controller layout as the Wii Virtual Console's; However, the controls can be customized to the players preference.