Baby Wario is Wario when he was a baby. In Yoshi's Island DS, he (and multiple other famous characters from the Mario franchise) will help Yoshi save all of the babies that were recently victims of a mass-kidnapping started by Kamek. He will join Yoshi's team in world 3, though will shortly leave due to his greedy nature. He eventually returns to help the babies one last time in World 5-8 to defeat Bowser.
Oddly, at GDC 2007, Charles Martinet, the voice of Baby Wario, seemed to have forgotten that he voiced him, as he was quoted saying how wishes to some day do a Baby Wario.