The Gerudo, a race first introduced in The Legend of Zelda: Ocarina of Time, were largely inspired by the Arabic and Egyptian civilizations in the medieval Middle East. This can be alluded to by the Arabic and Egyptian themed locations and sculptures that the series has has to offer, in addition to the original design of the Crest of the Gerudo resembling an Islamic star and crescent. This symbol can be seen throughout the original release of Ocarina of Time on blocks, floor switches, and even the Mirror Shield. The similarities to the Islamic symbol caused controversy, and was changed to a new symbol in all re-releases of the game.

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.

In the Hyrule Castle courtyard, in one of the windows you can see pictures of Mario, Luigi, Yoshi, Peach and Bowser. In Ocarina of Time 3D, the pictures were replaced with a Mario level background with warp pipes and blocks.

The sound of the warp whistle from Super Mario Bros. 3 (which uses the same sound as the recorder from The Legend of Zelda) can be heard in the title theme.

The sound of the Recorder (also known as the Flute or Whistle) In The Legend of Zelda was later used as the sound for the Warp Whistle in Super Mario Bros. 3, and can be heard in the title screen theme of The Legend of Zelda: Ocarina of Time.

At the bottom of the pool inside the Lakeside Laboratory is a motionless shark behind a set of bars.

The characters Talon and Ingo are loosely based on Mario and Luigi.

At the fishing hole, if you cast your line just right, you can catch the shop owner's hat, revealing a bald patch on his head.

Malon wears a brooch in the shape of Bowser's head.

Although Majora's Mask is a direct sequel to Ocarina of Time, there was an officially licensed novel released set shortly after the events of Ocarina of Time. "Link and the Portal of Doom" was written by Tracey West and published by Scholastic in 2006 as part of the Nintendo Heroes series.

In the book, a mysterious portal suddenly appears in Hyrule which absorbs all things around it and threatens to destroy the land. Link and Navi have to travel across Hyrule to learn five parts of a song which will destroy the portal.

Although officially licensed by Nintendo, it's considered to be non-canon.

After acquiring the three Spiritual Stones and obtaining the Ocarina of Time from Zelda, if players head straight to the Back Alley of Hyrule Castle Town, they'll find a fatally wounded Soldier. If players talk to him, he'll tell how Ganondorf betrayed the King and that he was injured trying to fight Ganondorf's men so Zelda and Impa could flee. He tells Link to head to the Temple of Time and dies soon after.

If players try to talk to him again, a message will appear saying "He's not moving anymore...."

At one point in the Spirit Temple in The Legend of Zelda: Ocarina of Time, Link must fight an Iron Knuckle that turns out to be a hypnotized Nabooru, who returns to her senses after being defeated. By clipping the camera through her Iron Knuckle armor, you can see her head modeled underneath her helmet, likely to facilitate the post-defeat cutscene where her armor falls off.

Furthermore, every other Iron Knuckle in the game also has a placeholder Gerudo head modeled underneath the helmet. While much of the head's face is obscured by chainmail, the details that are present indicate that it is most likely an early version of Nabooru's design; of note is that the head's hairstyle is closer to that seen on Gerudo Village's guards, implying that this element was reused for them when Nabooru's design was revised to the version seen in the final game.

This placeholder head is also present inside the Iron Knuckles that Link encounters in The Legend of Zelda: Majora's Mask, due to that game reusing many assets from Ocarina of Time.

In the German version, the carpenters are named John, Paul, George & Ringo, after the 60's British pop group The Beatles.

When starting development on Ocarina of Time, Nintendo weren't sure how large of a game they'd be able to make with the Nintendo 64's memory restrictions. Miyamoto even considered structuring the game in a similar fashion to Super Mario 64, with Ganon's castle being the hub. The Forest Temple with Ganon's doppelganger jumping in and out of paintings was an idea carried over from that period of development.

After slashing a sign with your sword in Ocarina of Time, playing Zelda's Lullaby while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Majora's Mask with playing the Song of Healing.

It's speculated that the forest and water temples in Ocarina of Time were originally wind and ice temples. The symbol on the Water Medallion from the Water Temple appears to have a snowflake on it, and the Forest Medallion design resembles a fan. This connection is further supported by the interior of Ganon's Tower, which is based on different temples. The Forest Temple portion of the tower has a wind puzzle based around fans, and the Water Temple portion of the tower is based on ice.

In the German version of Ocarina of Time, if you speak to Princess Zelda while wearing the Keaton mask, she will say:

"Was bist du denn? Ach, du bist eines dieser goldigen kleinen Taschenmonster, oder?"

Which roughly translates into:

"What are you? Oh, you're one of those golden little pocket monsters, right?"

Referencing the visual similarities between the mask and Pikachu.