During the American Civil War, President Lincoln and his Administration suspended the right to a jury trial by suspending the writ of Habeas Corpus and using military commissions to try civilians. This study first explores the suspension of the writ of Habeas Corpus. It then discusses 262 military commission cases, selected for comparative study. These cases took place between 1861 and 1866. The purpose of this study is to bring to light a little-known aspect of the Civil War, the use of military commissions to try civilians, for use as a tool in future studies, and show that the suspension of the right to a jury trial in the past connects to current issues involving suspended civil liberties.