Mother 3 was originally going to be a 3D game for the Nintendo 64 DD add-on. Dubbed "Earthbound 64" by fans, the game was delayed several times due to the little experience the development team had with 3D games. The game would have possibly utilized the N64 DD's features and would also possibly use Mario Artist to create new in-game character faces. The Rumble Pak was also considered to be used during battle sequences. Due to the commercial failure of the N64 DD, the game was canceled but later recreated for the Game Boy Advance.

An interview by creator Shigesato Itoi reveals that if Claus managed to pull the final needle Spoiler:to awaken the dragon, then all of existence would have been erased, including the dragon itself.

In Chapter 7, when a hooded Mr. Saturn gives you back the Courage Badge, he says goodbye to the player and walks a few spaces offscreen where it is supposed to stop and disappear. However, due to a bug, he remains in that spot, just a few spaces away from the player. Itoi liked this bug, so he decided to keep it there and write some text for him.

The "Ok desu ka" that sounds on the Character Naming screen is voiced by Shigesato Itoi, who was tricked into saying it into a hidden tape recorder by Hirokazu Tanaka, the music composer for the Mother 1 and Mother 2.

Mother 3's Main Theme "Love Theme" wasn't created until far into the game's development. Itoi said that it didn't even exist in December 2005, a mere 4 months before the game's release.

Shogo Sakai was the only person in charge of all the music in Mother 3, which count up to being 250 songs. Itoi realized even before he started development that he couldn't just request an outside musician and wanted someone who would have a lot of time to work on the project.

There are two inaccessible rooms in the Toilet Dungeon in Chapter 8: one where water seeps from the bottom of the door and another where a man rushes in and locks the door. By cheating, one can see what's inside these rooms, which is an overflowing toilet for the first and a bathroom full of toilet paper for the second.

Shigesato Itoi stated in an interview that, due to Porky's immortality, he will still be alive 5.5 billion years after the date at which the interview was taken, when the world has ended, stating that "the grief of that is incredibly depressing to me. It's amazing... Porky is truly a poem in himself.."

In one of the caves, a simplistic map of Japan can be seen on the floor.

When fighting Mr. Passion or Lord Passion, his background music contains samples from Famous Composers, such as Beethoven's Symphony No. 5 in C Minor and Tchaikovsky's Piano Concerto No. 1 in B flat Minor.

Footage of the game taken during its development period on the Nintendo 64DD shows Ness, the protagonist from EarthBound, to be a playable character. The footage shows Ness riding the Pork Bean through a desert area, as well as him running through a jungle.

There is an unused favorite food item that heals 300 HP to a single party member, which can be bought for 200 DP. Suggesting that the favorite food was planned for inclusion at some point of the game.

Claus has over 150 unused sprites, the most out of all the characters in the game, including full running and walking animations in a bathing suit.

The enemy, Gently Weeping Guitar, is a reference to The Beatle's song, "While My Guitar Gently Weeps".

Shigesato Itoi stated in an interview that Tanetane Island and its hallucinations were based on his affinity for the television shows "Twin Peaks" and "Lost".

In Chapter 8 during Leder's story, the music that plays, "Leder's Gymnopedie", is both named after and an adaptation of Erik Satie's "Gymnopedie No.1"

The track "The Water's Great", that plays while in a hot spring, has the same melody as "Open Sesame Tofu", which plays during The Wess Dance to open a few doors in the game, but is much slower. Although The two pieces of music and the events they accompany seem to be completely unrelated.

Within the game's files is a low-quality picture of the Summit Inn Cafe, a famous roadside diner built on Route 66 in California. The image was most likely used for graphics testing, though it might have also been used as a reference for the Dur-T Cafe seen in Chapter 5.

The Game Boy Advance contains the original Game Boy and Game Boy Color's CPU, the LR35902, for backwards compatibility purposes. In Mother 3, the song "Porky's Porkies" uses only the original DMG processor, and the inside variation of "No Eating Crackers in the Cinema" also primarily uses it, though the latter also uses a sampled bass line.

Mother 3's official soundtrack, Mother 3+, contains a remix of the song "Snowman". This remix was reused 2 years later for Super Smash Bros. Brawl. The 2 tracks are near identical, with the only major difference being the intro to the song. The Brawl version uses a choir for the beginning, while Mother 3+ uses a wind sound in its place. The Brawl version also adds a drumbeat to the song on its second loop.