Dr. Mario is a puzzle game where you play as Dr. Mario, who must drop differently coloured pills onto viruses to remove them from the bottle. The goal is to align three pills of the same colour with a virus of the corresponding colour or any combination of pills and viruses totaling four or more. This will remove both the aligned pills and the virus from the bottle.
The level is cleared when there are no viruses left, while the game is over when the pills reach the top and Dr. Mario can't drop any more pills. The game features three main modes: normal mode, a time trial, and a two-player battle mode to see who can remove the most viruses.