The Nintendo 64, PC, & PlayStation 2 versions of the game contain secret minigames that the player can play.

For the N64 & PC versions, the minigame 'Menezis' is a 2D space shooter where the player controls the letter E firing and dodging projectiles from the letters X, O, & the number 8. This minigame is also included in the Dreamcast version, but was only available as downloadable content at the time of that version's release and can no longer be played without hacks. For the other two versions, it can be unlocked in different ways:

• For the N64 version, hold C-Left while quickly and repeatedly pressing the A and B buttons simultaneously during the credits.
• For the PC version, type 'SHOOTEMUP' during the credits roll or wait after the credits roll.

The PlayStation 2 version contains a different minigame, 'The Schplong', a game that resembles Pong. The player controls a sliding blue bar on the left of the screen and must score to win against the computer player. This can be activated in the level The Iron Mountains during the cutscene where Rayman is riding the hot air balloon. Pressing the Square or Circle button 15 times while the cutscene is playing activates the minigame.

In early copies of the PC version, the game would sometimes mistakenly display the "CD missing!" message. The game is still fully playable, however, with the drawback of the error message obstructing most of the screen.

In the final phase of the Tomb of the Ancients (outside the door to the Clark boss fight), there is a secret passage leading to a blocked-off area showing a campfire party with a dancing Grand Minimus, two baby Globoxes playing drums, and a large character named Jeff, a depiction of Ubisoft lead 3D programmer François Queinnec, playing guitar.

This secret was originally created by an unknown artist and developer Arnaud Guyon for the Nintendo 64 version of the game and can be accessed with the following combination: Hold L + R while pressing A/B/A/B/A/B. This will cause a crate to appear that can be used to enter the passage. When the PC version of the game was developed, this cheat was changed to standing in a specific spot in front of the passage and typing "playjeff" to make the crate appear. Guyon posted details of this variant of the Easter egg on his website in 2002, but it would go undiscovered by players until 2018.

This area can also be accessed in the Dreamcast and Nintendo 3DS versions of the game using the following combinations:
Dreamcast: Press A/B/X/Y/X/Y
Nintendo 3DS: Press B/Y/D-Pad Right/D-Pad Left/D-Pad Right/D-Pad Left

In the Nintendo DS, iOS and PlayStation 2 versions of the game, the hidden area is available, but can't be accessed, either due to the respective buttons not being available to press or because the cheat was disabled. In the PlayStation version, it does not appear at all.