The Master Sword being a sword that would get pulled out from its pedestal by those chosen appears to be derived from the Arthurian Legend of Excalibur, also known as the "sword in the stone". Similar to how King Arthur was divinely chosen to be able to pull out Excalibur, Link was given the power by the Goddesses to pull out the Master Sword. Because of these similarities, the Master Sword was renamed to "Excalibur" in the French localizations of The Legend of Zelda: A Link to the Past, The Legend of Zelda: The Wind Waker, and The Legend of Zelda: Twilight Princess.

The model for Epona can be found outside the boundary for an arena in Faron Woods Spoiler:that gets extremely infected by Twilight later on, suggesting that the developers were thinking of allowing the player to call and use her in that area before dropping the idea.

There is an unused enemy in the game's data named "Meter Giant". It was likely a place holder model for measuring other objects in game.

Midna's voice clips are made up off scrambled pseudo-speech. When unscrambled, it is revealed that she is actually speaking in English.

If the player attacks a Cucco enough, they will eventually take control of the Cucco. This breaks the conventions of attacking Cuccos in The Legend of Zelda series, as they would usually just get attacked by a flock of them.

The Fused Shadow from Twilight Princess bears a striking similarity to Majora's Mask. It is highly possible that Majora's Mask was created by the same tribe who made the fused shadow, known as The Interlopers. This is made even more probable due to the fact that Twili are seen frequently wearing masks, as Zant and his Guard both wear masks, as well as the Shadow Beasts. In addition, when you steal the Ordon Shield from the village in Twilight Princess, Midna attempts to wear it on her face, like you would a mask.

In early trailers of the game, Midna had blue and orange hair instead of the solid orange hair visible in the final version. Also, Link had the ability to dive as if he had equipped the Zora armor while wearing his regular tunic, but his regular swimming abilities are limited in the final game.

Sheik was planned to appear in Twilight Princess, but was cut from the game. This unused design was later used for Super Smash Bros. Brawl.

The attached artwork is from the Hyrule Historia.

Room 49 of the Cave of Ordeals contains 3 Darknuts to defeat the first time around. If you play through the Cave of Ordeals a second time and reach this room, a 4th Darknut will be added as an additional challenge.

Darknuts have a low-quality, low-polygon, and mostly featureless face underneath their helmets that cannot be seen in normal gameplay.

Using the lantern inside of Barnes' Bomb Shop will trigger a cutscene where Barnes will activate a sprinkler to put out the lantern.

In early pre-release screenshots and in the first playable demo of the game, Link could ride a canoe in Ordon Village's river, although this feature was removed from this area in the final game. These screenshots also suggest that the river was planned to be bigger and potentially a Fishing Hole before being sized down, although Hena's pond in the final game bears some resemblance to this area.

Interestingly, an unused yet fully implemented feature for canoes allows dogs to hop on and ride with Link on the bow, and then hop off when returning to land. However, dogs and canoes do not appear together in any location in the final game unless they are modded in. Seeing as Ordon Village has two dogs inside different houses and was originally meant to have canoes, it's possible this place would have done more with this feature before it was scrapped.

A popular image macro known as "Gaijin 4koma" (JP: "4-frame foreigners"), depicting a group of fans reacting with indifference to something and then excitement, used to compare the meme editor's and/or popular opinions on two particular subjects, consists of two photos taken by IGN of their reporters during Nintendo E3 presentations in the early 2000s. The excited photo being towards the announcement of The Legend of Zelda: Twilight Princess in 2004, while the indifferent photo was taken during the announcement of Pac-Man Vs. in 2003.

While Navi does not appear in Twilight Princess, she has unused lines and sound effects which can be found in the game's data, including those which may have been intended to be heard from the Wii Remote speaker in the Wii version.

According to Eiji Aonuma, The Legend of Zelda: Twilight Princess was inspired by "The Lord of the Rings" movie trilogy, as he wanted the game world to be vast enough to match expectations fantasy audiences had at the time:

The character design of Purlo, who runs the STAR game in the thoroughfare of Castletown, was directly based on Tingle. According to Eiji Aonuma, he is what Tingle would look like if he was made with a realistic design.

There is a minigame Link can play with a Cucco in the Hidden Village towards the end of the game called Cat Hunt. The object of the minigame is to find 20 cats hidden throughout the village, and Link will be rewarded with a Piece of Heart. In the English translation of the game, the cats have no names and all say "Meow! What fun, meow!" when caught, but in the French translation they each have personal names and custom dialogue.

The fisherman from Ocarina of Time can be seen in a photo at Hena's fishing hole. Hena thinks she is related but she "can't exactly PROVE it." She also scratches like the fisherman, further linking them together.

The 7th dungeon of Twilight Princess, "City in the Sky", is speculated to be based on a painting called "Another World" by M.C. Escher. The creatures, seen on the walls in the painting resemble the Oocca from the game. In the Twilight Princess dungeon, the Oocca are found running on the walls and floor.

Fyer has a Bullet Bill from Super Mario Bros. on his right sleeve.