The Alton prison opened in 1833 as the first Illinois State Penitentiary and was closed in 1860, when the last prisoners were moved to a new facility at Joliet. By late in 1861 an urgent need arose to relieve the overcrowding at 2 St. Louis prisons. On December 31, 1861, Major General Henry Halleck, Commander of the Department of the Missouri, ordered Lieutenant-Colonel James B. McPherson to Alton for an inspection of the closed penitentiary. Colonel McPherson reported that the prison could be made into a military prison and house up to 1,750 prisoners with improvements estimated to cost $2,415.
The first prisoners arrived at the Alton Federal Military Prison on February 9, 1862 and members of the 13th U.S. Infantry were assigned as guards, with Colonel Sidney Burbank commanding.
During the next three years over 11,764 Confederate prisoners would pass through the gates of the Alton Prison. Of the four different classes of prisoners housed at Alton, Confederate soldiers made up most of the population. Citizens, including several women, were imprisoned here for treasonable actions, making anti-Union statements, aiding an escaped Confederate, etc. Others, classified as bushwhackers or guerillas, were imprisoned for acts against the government such as bridge burning and railroad vandalism.