The Master Sword was named after King Arthur's legendary sword "Excalibur" in the French version of The Legend of Zelda: A Link to the Past. The name Excalibur would also be used in the French versions of The Legend of Zelda: The Wind Waker and The Legend of Zelda: Twilight Princess.

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.

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:

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.

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.

Twilight Princess is one of the few Zelda games that does not have a magic meter. As such, there is no need for Green Chu Jelly, which is an item used to refill magic in other Zelda games. However, in the Wii version, it is possible to obtain Green Chu Jelly through normal means. But it is only possible once, in the "Cave of Ordeals", room 19. Carefully kill all of the purple Chus and let a Blue Chu and and Yellow Chu merge. Kill it and then scoop up the remains with a bottle. Link will now be holding a bottle of Green Chu Jelly. It has no text, description or effect whatsoever. However, performing this trick in the GameCube version produces a Purple Chu instead.

Link made his first right-handed appearance in Twilight Princess for Wii. Up through Twilight Princess for GameCube, Link had traditionally been left-handed, but with the introduction of motion controls, director Eiji Aonuma decided to make him right-handed so it would be more comfortable to "swing" the sword with your right hand (which is how most people were playing). Instead of re-doing Link's model though, the Wii version of the game was simply flipped horizontally, reversing the positions of everything from east to west.