Jr. Troopa from the first Paper Mario can be seen flying in the background of a post card from Zip Toad.

In the Spanish version of Paper Mario: The Thousand-Year Door, one of Rawk Hawk's lines is slightly changed to "¡Los aficionadillos deberían quedarse en casa jugando Super Smash Bros. Melee!" (translation: "The weaklings should stay home playing Super Smash Bros. Melee!") after having defeated The Koopinator. In all other versions of the game "Super Smash Bros. Melee" is simply replaced with "video games".

Bobbery's early design was actually a Soldier, until it changed into a more of a pirate themed appearance.

The color of the Yoshi that hatches from the egg in the Glitzville Glitz Pit depends on the amount of time that passes between Mario acquiring the egg and the point in the game where it hatches. The Yoshi is always green in official artwork but can also be red, blue, orange, pink, black, and white.

Luigi's partner, Screamy, is based on the original design of the Smorgs.

In the Spanish translation of the game, Chapter 3 "Of Glitz and Glory" is titled "el rey de los luchadores". When translated, this means "the king of fighters", possibly referencing The King Of Fighters series.

An unused "Coming Soon" image is present in the game's data. Instead of the game's final title, it uses the name "Paper Mario 2".

After Paper Mario: The Thousand-Year Door's announcement in 2003, some Mario fans incorrectly believed that the character of Madame Flurrie was going to be the ghost of Bowser's wife, based off of her character design and Japanese name. This is due to Flurrie's Japanese name, "Cloudia", sounding a lot like "Clawdia", a popular urban legend name for the Koopalings' mother supposedly created by the Mario fan website "Lemmy's Land", as well as Flurrie sharing a hair style with Ludwig and lip-shape with Wendy, who were at the time considered Bowser's children by Nintendo.

On June 12, 2008, the film studio Morgan Creek Productions filed a lawsuit against Nintendo of America, alleging that Hans Zimmer's song "You're So Cool" from the 1993 film "True Romance" was used in a commercial for Paper Mario: The Thousand-Year Door without permission.

Six days later, Morgan Creek dropped the lawsuit without comment. Nintendo would later release a statement revealing that the day before the lawsuit was dropped, Leo Burnett, their advertising agent, gave Morgan Creek "a copy of a music license entered into between Leo Burnett USA, on behalf of Nintendo of America and Morgan Creek, for licensing of the song."

At one point, the W Emblem was going to be purple. This would imply that when Mario equips the W Emblem, it was originally going to make Mario’s clothes transform into Waluigi’s clothes, as opposed to this happening by equipping the L and W Emblems in the final game.

Within the GameCube version's data are graphics for an earlier Vivian design depicting her with a shorter body and a flame on the tip of her hat. Concept art included in the Nintendo Switch remake reveals that the latter trait was part of an early design for all three Shadow Sirens, with Beldam and Marilyn also having a shard of ice and a lightning bolt at the end of their respective hats. This concept art additionally depicts the Shadow Sirens with black skin, which was changed to purple by the time the early Vivian sprite was created.

The gender identity of the party member Vivian is inconsistent between different language translations of the original game. In the Japanese version, Vivian identifies and presents as female, but is described by other characters in the game as actually being an effeminate-looking male, aligning with common media depictions of transgender or gender non-conforming characters at the time, but not explicitly referring to Vivian as such. A rough translation of the Japanese text for Vivian as a party member reads:


The French version directly carries this over and additionally describes Vivian as a boy pretending to be a girl, while the Spanish version describes Vivian as a boy who looks like a girl. However, according to former Nintendo of Europe translator Pol Roca, Vivian's Spanish name "Bibiana" was intended to be a reference to the Spanish transgender actress Bibiana Fernández, who starred in the 1977 film Cambio de Sexo (or Sex Change).

The English and German versions remove any references to being transgender or gender non-conforming, implicitly portraying Vivian as a cisgender woman with "a bit of an inferiority complex". Instead of being bullied over her biological sex, her sisters instead belittle her for her appearance.

The Italian version of the game on the other hand explicitly depicts Vivian as an openly proud transgender woman, with the localization reconfiguring her relationships with gender identity and her sisters by having Marilyn and Bedlam's bullying being rooted in jealousy, traits which are absent in the Japanese script:


The English release of the Nintendo Switch remake follows the Italian version of the original game in unambiguously describing Vivian as a transgender woman, most prominently featuring a line where Vivian states that "it took me a while to realize that I was [Marilyn and Beldam's] sister... not their brother." It's currently unknown if Vivian's portrayal in other translations of the remake has changed from the original release.