At the Toad Town train station, there is a blue Toad who tells Mario that after he defeats Bowser and restores peace to the Mushroom Kingdom, he has something else he wants to tell him. However, no such event can be triggered as it's impossible to access the train station after defeating Bowser, making the line pointless as you cannot talk to him again. It's possible that this was meant to be part of content found in the post-game, but was cut during development.

If Mario manages to defeat Bowser by hacking/cheating at the very beginning of the game, the game will crash as developers never intended for that outcome to happen.

When Gold Li'l-Oinks leave the farm in the Japanese game, they drop Jelly Shrooms (restores 5 HP and 50 FP). In the U.S. version, Gold Li'l-Oinks drop Ultra Shrooms (restores 50 HP). This gives you a way to collect an unlimited amount of Ultra Shrooms, whereas you can only find five Ultra Shrooms total in the Japanese version.

If the player uses Spook on Jr. Troopa, he'll generate a "?" bubble before saying "Don't underestimate me, Mario! I'll never be be scared away by such a cheap trick! No way! Never!" This message contains a typo by saying "be" twice consecutively.

Under the Smash Attack mini-game room, there are 10 unused Luigi sprites. Since the mini-game has Mario searching boxes for 10 portraits of Princess Peach, it's possible that the game's goal was originally to find Luigi in the boxes 10 times, and the developers simply forgot to remove the Luigi sprites.

The Koopa Bros. are an obvious reference to the Teenage Mutant Ninja Turtles. Both the Koopa Bros. and the Teenage Mutant Ninja Turtles are turtles and wear bandannas around their heads. The Koopa Bros. also speak in skater slang similar to the Teenage Mutant Ninja Turtles.

It is possible to get your partner Kooper to give Mario a kiss with a glitch in the Ice Palace chapter. During a puzzle that requires the player to discover the real Bombette amidst several imposters, the player can leave the room and re-enter it by clipping through a wall. Upon re-entering, if you have changed your partner to Kooper, Kooper will kiss Mario upon solving the puzzle instead of Bombette as intended. Doing this with partners other than Kooper causes the game to crash.

In Dry Dry Desert, north of Kolorado's camp you can find a yellow block which when hit multiple times will reveal three hidden '?' blocks which subsequently give you a Shroom (1 hit), Super Shroom (10 hits) and Ultra Shroom (100 times). This block keeps track of how many times you hit it and has a maximum unsigned four byte value of 4,294,967,295, which means that hitting it more than that amount would reset the blocks and spawn them over the existing ones allowing you to get the Shrooms again, which would take 36.29392 years to reach. Hitting the block another 4,294,967,295 times would reset it again, causing the hidden blocks to spawn over the existing ones again. Continuously repeating the process until the game freezes would take just over 416 years to achieve.

Minh T., the flower loving Toad in Toad Town Garden, is named Lip in the Japanese version. Lip was also the name of the flower fairy protagonist in the SNES game, Panel de Pon (Tetris Attack internationally). Both characters share a love of flowers and even share the same yellow, green and pink colour scheme.

The name of Herringway, the famous murder mystery author in Shiver City, is a pun on herring, a type of fish penguins eat, and Ernest Hemingway, a famous author.

The Japanese symbols on the Toad Town Dojo's billboard read "way of the old man".

Early screenshots for the game show a different art style for Mario. The old design had Mario with sclerae in his eyes instead of simple black dots in the final.

Whacka has an entry in the enemy name table and a tattle. Based on the tattle, it seems that earlier in development, instead of disappearing after being hit enough times, he would attack.

An enemy known as "Albino Dino" appear as statues in the "Crystal Palace" but are never fought. They can still be fought by using GameShark Codes, and Goombario actually has tattle dialogue for them. They only have one attack, a charging ram that damages Mario.

Paper Mario was originally slated to be released on the Nintendo 64 Disk Drive. However, due to the Disk Drive's commercial failure, the game was later released on the cartridge format.

There is an unused enemy called "Aqua Fuzzy". The only remnants of it that have been found in the game's code are its name and the blue palette that would be applied to the fuzzy sprites.

There is an unused sprite that appears to be Princess Peach kissing someone. It was most likely Peach kissing Mario during the descent of the the castle during the game's end.

The names of the two members of the Dojo (Chan and Lee) are references to the famous martial artists/actors Jackie Chan and Bruce Lee.

There was once an "Anger's Power" badge in the beta for Paper Mario. It would cause Mario to gain a dark red tinge of color, and pose angrily. Mario's turn would be controlled automatically in battles, while the partner is controlled by the player. Mario's attack would increase by 2, but is AI neglects common sense, such as jumping on top of spike enemies. The effect is very much similar to the common "Berserk" status of many RPGs.

Chuck Quizmo and his assistant, Vanna T., are possible references to game show host, Chuck Woolery, and hostess, Vanna White.

Paper Mario was also originally going to be named Super Mario RPG 2, though due to complications involving Square Enix, the makers of Super Mario RPG: Legend of the Seven Stars, the name was changed to Super Mario Adventure and later Paper Mario.

In Boo Mansion, if the player goes through the door across the hall from the entrance and jump in the jar inside, Mario will come out of the jar looking like his original 8-bit sprite from Super Mario Bros.

Waiting an additional 10 seconds after the jingle that plays on chapter title cards will cause a complete version of the Super Mario Bros. theme song to start playing.

Luigi keeps his diary in a secret basement under his and Mario's house. If you manage to read the entries, you can find one entry reveals that Luigi is afraid of ghosts, and another where he says he wants to have the lead role in his own adventure. These diary entries are referencing Luigi's Mansion, which was in development at the time.