On the World Map pause screen after finishing the game, if you press L/R/L/R/X/X/Y/Y, a secret Challenge Mode will be enabled that disables scrolling backwards in levels, making the gameplay more similar to Super Mario Bros., Super Mario Bros.: The Lost Levels, and Super Mario Land. Inputting this code again on the World Map pause screen disables this mode.

It may have been planned for the player to get the blue shell by defeating a blue koopa and then ground pounding the shell. This idea was included in the VS. mode, but the player didn't have to use a ground pound.

Tapping letters as the credits roll will make unique sound effects play. These effects are heard throughout the game, and each letter has its own sound (except for letters D and E, which share the same sound). The letter Q is never seen during the credits and thus has no sound.

The file "hatena_switch" is the Question Switch model from Super Mario 64 DS, and may have been used in an early version of the game. The switch is a 2D graphic in the final game.

The name "/script/game.bmg/msg 7" has text that says "You can't save here. Do you want to quit?" which is only used during certain undetermined circumstances.

New Super Mario Bros. was originally meant to have a two player co-op mode. This idea was not implemented until 2009, when New Super Mario Bros. Wii introduced four player co-op. Eventually, this two player mode found its way into New Super Mario Bros. 2 on the 3DS in 2012.

The Bottom Screen looked different in some prerelease builds. The coin and time HUD were placed there originally, there were 3 item slots instead of one, and the Star Coin's HUD was missing. The head of the pipes were also slightly different.

A crash dump screen, used for debugging, still exists within the US retail copy of the game. It can be accessed by inputting a series of button combinations after crashing the game. It displays build information, the reason for the crash, and a stack dump.

There is a reference to Super Mario Sunshine in the game's manual which reads: "Didn't Bowser Jr. once think Princess Peach might be his mother?" In Super Mario Sunshine, the story involves Bowser Jr. kidnapping Peach because he thought she was his mother.