Autogen is the complicated system that automatically generates notes for each song.

Notes are generated by distinct beats (usually bassy, quieter sounds are easier to generate notes from) and cannot be generated at a rate faster than 285 notes per minute (i.e. 285 bpm). The fastest continuous stream of notes is seen in Kick Drum Metronomes 280 bpm. Kick Drum Metronomes 290 bpm generates notes at 285 bpm at maximum but they cut off at regular intervals as the game cannot keep up with the beat of the song.

Single notes and double notes are randomly generated. The number of double notes and Sushi placements are random but spread across the step chart approximately evenly. Attack placements are randomly generated depending on the player's current position. Attacks cannot be generated if the player is in first place.

Notes cannot be placed in Freestyles. Invisible notes can occur around Difficulty bars resulting in the Bar Glitch. The Freestyle bug can occasionally occur resulting in large blank spaces in a song.