Whirlwinds first appeared in Mario & Luigi: Superstar Saga. If Mario & Luigi walk into one while doing a spin jump, they will be sucked into it. While inside, they can be launched further than they can normally go. In Joke's End the steam the broth creates can be spin jumped into to create Whirlwinds. Also, if Luigi hammers Pump Mario to make him spit water at a whirlwind, this can help put out candle fires to go to the next room.
The Whirlwinds reappear in Mario & Luigi: Partners in Time, Mario & Luigi: Bowser's Inside Story, Mario & Luigi: Superstar Saga + Bowser's Minions, Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey. They served the same purpose in these games as in Mario & Luigi: Superstar Saga.