In Dr. Mario World the player controls capsules and lines them up with viruses to eliminate them. The player must match at least two same colored capsule units with the virus to eliminate it. The player can rotate the capsules and move to place them. They cannot move the capsule farther back down the screen though. Each capsule has two units. If only half the capsule is needed to destroy a virus (or three or more capsule units in a row are formed) the player can move the other capsule. Once a capsule is place on the board it slowly rises. Other capsules can be placed on the board and moved ahead of these capsules to give the player more control.
There are a number of characters including Dr. Mario Dr. Bowser Dr. Peach and more. These are the three characters initially available. They each have their own unique unique skill if you fill the skill meter. They also each have their own set of assistants. The player can use up to two assistants at a time and they provide an in game bonus.
The game has a world map of normal stages that are linear and there is a versus game where you can play other players.