The game features a crash debugging tool that allowed the developers to find out information as to why the game has crashed. This is still present in all the Nintendo 64 releases, and can be accessed by inputting a series of button combinations after crashing the game. Information about the game and the environment that was present during the crash will be accessible from this screen.

The Version Info screen, however, not only has information about when the game's version was compiled, but also a message which reads, "I LOVE YOU".

Charles Martinet has expressed interest in providing the voice of Link:

The track used for The Legend of Zelda: Ocarina of Time commercials is "Riddle of Steel" from the 1982 film Conan the Barbarian. This same song was also later used for The Legend of Zelda: Twilight Princess E3 2004 trailer.

In some trailers of different Alpha/Beta-builds for the game, it can clearly be heard that both Navi and Link had different voice actors. It is also apparent that Navi had different lines of dialogue.

The Plaque that appears in Dodongos Cavern is the exact same one on the fountain in Super Mario 64.

It was originally planned for the Great Fairy to be blue and white. The beta model can be found in the game's data.

In the Hyrule Castle Courtyard, there is a window to the left when you first enter. It's empty, save for a plant. If you take out your slingshot and fire at the plant, it will trigger a guard to appear and say "Hey You! Don't cause any trouble!" then throw bombs at you.

In the Master Quest version of the game, the Water Temple has an extra key that cannot be used. This is due to the fact that a flag in the game's code is accidentally set when Link defeats the three Stalfos in the room with the three dragon heads. This was fixed in the 3DS version.

A time paradox is created in Ocarina of Time. According to Guru Guru in Kakariko Village, Link played the Song of Storms as a child to speed up the windmill, yet Link is taught the song by Guru Guru as an adult. Because of this, the question of who originally composed the song remains a mystery.

Further proof that the Water Medallion was meant to be the Ice Medallion can be found in the fight with the Sorceress Sisters. Kotake's attack symbol (fire) has the same design as the fire medallion and Koume's attack symbol (ice) has the same design as the water medallion.

In Link's house there is a picture showing link with a fairy fighting a monster. Due to the fact that it looks like a dinosaur some have speculated it to be King Dodongo.

In some early versions of the game red blood can be seen throughout. The color was changed to green in later versions.

By using Gameshark codes, you can activate cutscenes that were originally going to be in the game. One is an early version of the prologue cutscene which takes place at sunset rather than night and three other cutscenes that take place in the Temple of Time, in which each cutscene focuses on each Spiritual Stone.

The name of Link's horse, Epona, when translated from Gaulish means "Great Mare" and is the name of the Celtic God of horses, donkeys and mules.

If you go into the room with the giant statue inside the Spirit Temple, and aim the Hookshot at where the nipples would be, you will find that you can grapple on to them. It's possible this was a joke by Nintendo.

Throughout the game you may see a symbol that looks like a crescent moon and a star. This symbol can be found on blocks, floor switches, and even the mirror shield. This symbol has caused some controversy, as the moon and star resembles an Islamic symbol. In all re-releases of the game, it has be changed to a new symbol.

According to an interview with Yosiaki Koizumi in the 225th issue of Nintendo Power, the battle against Ganon would revolve around Link having to scale his body, which would've been gigantic at the time (similar to boss battles in Shadow of the Colossus). However, it was later changed due to how players could be confused in the fight (as they would never see Ganon's entire body), and rendering his colossal body at a steady framerate would've heavily strained the N64's hardware. The concept was later recycled for the Megaleg battle in Super Mario Galaxy.

Joelle, Meg, Beth and Amy, the poes in the Forest Temple are named after the main characters from Little Women, Meg, Beth, Amy and Josephine.

The music for the Fire Temple once had chanting of an Islamic prayer as a part of the background music. The chanting was a stock sound effect from a sound library collection called "Voice Spectral - Volume 1" released by 'best service', and it also showed up in games like Cruis'n World for the Nintendo 64 and Kakuto Chojin: Back Alley Brutal for Xbox. Seeing the problems it could have caused, Nintendo changed it, and the updated version of the Fire Temple replaced the chanting with the wails and moans from the Shadow Temple's music.

There are several signs in Ocarina of Time that you can cut. In the Nintendo 64, Gamecube and Wii versions of the game, you can cut them diagonally. The 3DS Version of the game only allows you to cut them vertically and horizontally.