According to an interview with Shigeru Miyamoto conducted while the game was still in development, Navi was originally intended to have romantic feelings for Link and was even jealous of Princess Zelda. Though it seems that these details were left out in the final game.

In early trailers of the game Link's bombs were slightly different. They were more round and a much darker blue.

In early versions of the game Sheik's eyes were blue, but were changed to the red in the final version.

Eiji Aonuma started developing Majora's Mask because he had no interest in remaking new dungeons for Ocarina of Time's Master Quest mode.

The owl that follows Link throughout his quest Spoiler:is actually the light sage Rauru.

Epona, Link's horse, actually began as an idea discussed during development of Super Mario 64 to include a ridable horse in the game. While never included in Mario 64, the developers knew they would eventually include a horse in Ocarina of Time and planned for it from the very beginning.

A glitch called the "Wrong Warp" glitch can be used to teleport the player from the Deku Tree basement to Ganon's Tower, as well as several other locations in the game. This glitch can be used to complete the game in a very short period of time.

During development, Stalfos originally had less armor and a different sword and shield, among other minor cosmetic differences.

Zelda's Lullaby sounds extremely similar to the 1976 song "Concerto for Philodendron and Pothos" by Mort Garson.

The knight Link is fighting in the early Zelda 64 trailer uses the same texture as Metal Mario from Super Mario 64.

The bassline for the The Song of Storms sounds very similar to the bassline for the Castle Theme from Super Mario World 2: Yoshi's Island.

Taking out a Deku Stick near a group of butterflies and leading one away from the group will result in the butterfly turning into a Fairy.

Link was able to ride Epona into Hyrule Castle Town during later beta-builds of the game. This can be seen in various pre-release trailers. Why it was removed is unknown.

Changing tunics and using certain items while next to a Gerudo warrior can alter the color of the warrior's clothing to match a color value of an item currently equipped to Link.

When the game was in later beta-stages, the buttons had different functions compared to the final release. The functions of the A and B buttons were swapped when compared to the final version; Links sword was assigned to the A button, and the B button was for action commands. Also during this period, the action-button didn't involve rolling. Instead, it was context sensitive and would trigger things like jumps in combat or get information from Navi.

It's possible to use an empty bottle to reflect Phantom Ganon and Ganondorf's magic blasts back at them, similar to how the Bug-Catching Net can be used to reflect Agahnim's magic in The Legend of Zelda: A Link to the Past. Both items are used in their respective games to catch things, which are then stored in a bottle. Also like the net, there are some advantages to using the bottle: it has a slightly wider swipe and a more consistent motion than the sword.

After killing a Redead, any other Redeads near it will flock around the felled enemy and sit. It's speculated that the Redeads are either mourning the loss of a comrade, or are eating the dead corpse, explaining why it disappears.

The character Sakon can be seen running around the Hyrule Town Marketplace. If the player speaks to him, he will say "Huff huff! I'm late! I'm late! For a very important date!", a quote from the White Rabbit in the novel Alice in Wonderland.

In an early beta version of the game, there was a place known as the "Unicorn Fountain". This was originally going to be where Link was to get the Triforce, and the ability to shoot beams from his sword. It is believed that it was to be accessed through the normally unreachable underwater cave in Zora's Domain.

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".