During the Civil War, the island fort served as a prison for captured Confederate army and navy personnel, elected civil officials from the state of Maryland, and Northern political prisoners. The fort was commanded by Colonel Justin Dimick from 1861 to 1864. Dimick was noted for his humane and compassionate treatment of the Confederate prisoners held at the fort. Of over 1,000 Confederate prisoners at the fort, only 13 died there, giving Fort Warren a much lower mortality rate than any other prisoner of war camp (Union or Confederate) during the Civil War.