From the Wit and Wisdom of Abraham Lincoln, by Alex Ayres:

During the Civil War, President Lincoln granted pardons to many Union soldiers who had been given death sentences by military courts. But he was not unconditionally opposed to capital punishment. For example, he refused to lift the death sentences assigned to five convicted "bounty jumpers" - men who were paid by localities for enlisting and who then deserted after receiving their bounties.

Although he was often criticized for granting too many pardons, President Lincoln was responsible for ordering the largest mass hanging in American history - thirty eight Sioux Indians on December 26, 1862.

This tragic turn of events began in the summer of 1862 when starving Sioux Indians, furious about broken promises from the federal government, attacked several small settlements in Minnesota.

Most of the able-bodied men were off fighting in the Civil War, which left the towns vulnerable to attack. In the bloodiest of all the Indian massacres, at least eight hundred settlers were killed. The Indians quickly seized control of a 250-by-50-mile strip of land. Eventually, however, the Indian uprising was subdued by U.S. army troops under the command of General John Pope. Hundreds of Sioux were imprisoned in the military stockade.

A military tribunal was established and, after a hasty hearing, 307 Sioux warriors were condemned to die. But there were questions about the legal authority of the tribunal, and ultimately the matter was dumped in Lincoln's lap.

President Lincoln, as commander in chief, personally reviewed each of the 307 cases. Then he wrote an order for the execution of the 38 Sioux he judged to be clearly guilty of murdering unarmed citizens - commuting the death sentences of the rest.

A huge scaffold, twenty-four feet square, was constructed in Mankato, Minnesota, for the public hanging. On the morning of December 26, the condemned Indians mounted the scaffold. Ropes were looped about their necks, and as the platform gave way beneath their feet, a crowd of four thousand civilians cheered.

The ordering of this execution was one of Lincoln's least glorious achievements, and one that historians often whitewash, but it illustrates the hard decisions he had to make daily as president during the Civil War.