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During the Civil War, the fort was used as a makeshift prison to accommodate the growing number of Confederate political and military prisoners (soldiers and sailors) captured during the war. It was an ideal site for a prison because of its isolation on a remote island already staffed with Union soldiers—who quickly became prison guards. The fort, however, continued in its role to protect Boston Harbor with cannon fire if needed.
Prisoners began arriving in October 1861, barely 6 months after the fort was first occupied by Union troops. More than 2,200 prisoners were incarcerated at Fort Warren at some time during the conflict. Only 13 prisoners died of disease, and it was considered a relatively humane facility for the Confederate prisoners. Some officers were even allowed to have alcohol and the freedom to move about the fort during daylight hours.

Because of the prisoner exchanges and paroles, prisoners were coming and going throughout the war—until that practice was ended by General Grant. There were brief periods when no prisoners at all were at the fort.
Alexander Hamilton Stephens
The most important prisoner ever held at Fort Warren was Alexander Hamilton Stephens, the Vice President of the Confederacy. Stephens was captured in May 1865 and released in October 1865. He wrote a detailed diary of his confinement at the fort which is still available in paperback.

CSA Vice President Alexander Hamilton Stephens.

The lower room where Stephens was placed in solitary confinement during his first few months.
The Trent Affair
Confederate diplomatic envoys James Mason and John Slidell were captured on a British mail steamer, the Trent, by a Union warship and were taken to Fort Warren. This international incident became known as the Trent Affair. They were held at the fort from November 24, 1861 until January 1, 1862.
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| James M. Mason |
John Slidell |
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| The main room in the quarters where Mason and Slidell were believed to have been imprisoned. |
Some notable Confederate prisoners
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| General Richard Ewell |
John Regan, Postmaster General |
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| General Isaac R. Trimble |
General Simon Bolivar Buckner |
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| General Adam "Stovepipe" Johnson |
General Lloyd Tilghman |
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