All levels are randomized within sets (all levels with two exits within their own set and all boss levels within their own set).
To ensure completion, Turtle Zone Special can not be in Mushroom House's overworld location.

All levels with two exits (Tree Zone 2, Hippo, Space Zone 1, Macro Zone 1, Pumpkin Zone 2, Pumpkin Zone 3, and Turtle Zone 2) can have their exits swapped.
If all dual exit levels have their exits swapped, Hippo will not be swapped (as the top exit is more difficult to get to and more desirable) and whichever level is in Macro Zone 1's overworld location will not be swapped (to make the secret exit more desirable); if Hippo is in Macro Zone 1's overworld location, then it is swapped.

Bosses in boss levels, independent of boss level location, can be randomized.
Boss health can be randomized (in increments of 2: each pig can have 4 to 8 health, tatanga, witch, and each Wario phase can have 6 to 10 health, and bird, octopus, and rat can have 6 to 12 health - fireballs do 1 damage, jumps do 2 damage).

Enemies within each level are randomized, with some exceptions.
Most notably, enemies that interact with the background, such as bullet bills, can not have other enemies in their original location (but sometimes they can be in other locations).
Piranha Plants and Fire Piranha Plants are swapped in every level they appear for the exception of Pumpkin Zone 2, Pumpkin Zone 4, and Macro Zone 3, due to graphical oddities.

All standalone power-ups are randomized, except for Moneybags in Tree Zone 1 (their sprite ID matches an enemy in the level).
All question mark power-up blocks are randomized.
Power-ups in the Wario fight are randomized, and if using a DX ROM, a heart is a possibility.
Bonus bell game power-ups are randomized.
If doing one-hit knockout mode, all hearts and stars are removed.

Platforms in Tree Zone 4, Tree Zone 5, and Wario's Castle have been randomized, including the height of some platforms in Wario's Castle.

Music on the file select screen, overworld, in zones, and in each level has been randomized.
Music in levels can be sped up to match "hurry up" music (when there are under 100 seconds left on the timer).

Gravity has been randomized, so that levels can have either normal, moon, or space gravity (no matter what their original gravity was).
To ensure completion, gravity can not be changed in Pumpkin Zone 2 or Macro Zone 2, and Pumpkin Zone 3 can not have moon gravity.

Physics can be randomized, with Luigi and ice as options (if using a DX ROM, it will force you to play as Mario or Luigi in some levels).

Some levels can randomly become autoscrollers, and autoscrollers can be turned off.
To ensure completion, if Space Zone 1 has moon gravity it can not be an autoscroller, and if Space Zone 1 is an autoscroller then the midway bell is removed.
Some levels can have autoscrollers with the screen scrolling at double speed.
To ensure completion, if Hippo has moon gravity or if Mario Zone 3 is in Mushroom House's overworld location, neither of them can have fast autoscrollers.

Gambling costs on the overworld have been randomized and the graphics display question marks for the costs to the player.
The cost for the first pipe is between 20 and 125, the second pipe is between 100 and 350, the third pipe is between 250 and 600, and the final pipe is between 550 and 999 (all pipes are guaranteed to increase in cost).
If doing one-hit knockout mode, all costs will be 999.

One-hit knockout mode will disable soft resetting with Start+Select+A+B and exiting levels with Start+Select, plus start the player with zero additional lives, remove all hearts and stars from the game, and make all gambling costs equal to 999.

Credits are altered to have random facts provided by dadinfinitum and oh_deer and lyrics by iceplug.
The file select screen includes the seed number and flags, primarily for racing purposes.