Slavery was not completely abolished in the United States until after the Civil War. The Emancipation Proclamation only freed slaves in states taking part in the rebellion: "all persons held as slaves within any state [in which the people were] in rebellion against the United States." This did not include the border states which were slave states, but fought for the Union. Lincoln did not feel that he had the constitutional right to free slaves in non-rebelling areas of the country, until the Constitution was amended. Thus, even when generals declared the slaves in their military districts free, Lincoln overruled them. It was not until the ratification of the Thirteenth Amendment (1865) were all African Americans declared legally free.

Long before then, however, African Americans contributed to the efforts of the Union. Individual African Americans served the Union cause; including people like Harriet Tubman, who worked as a worked as an army cook, a scout, a spy and a nurse for the Union. African Americans, including Frederick Douglass, lobbied to be allowed to serve in the Union Army. Douglass, a noted orator and abolitionist, pointed out that African Americans fought in both the Revolutionary War and the War of 1812. Nevertheless, the Union would not allow Blacks to enlist. Finally, by late 1862, enlistment was so low that pragmatism won over prejudice, and Blacks were allowed to enlist. By the end of the Civil War, 186,000 African Americans fought for the Union, about one third of whom died or were reported missing.

The 54th Massachusetts Volunteer Regiment was the first black regiment recruited in the North. Col. Robert Gould Shaw, who led the regiment, was killed in a Union attack of Fort Wagner. The Confederates stripped his body and threw him into a mass grave, along with the bodies of the African American soldiers who had been killed. When Gould's father, a wealthy Massachusetts abolitionists, found out how his son had been buried, he said: "the poor benighted wretches thought they were heaping indignities upon his dead body; but the act recoils upon them ... We can imagine no holier place than in which he is." Sgt. William H. Carney, of the 54th Massachusetts, became the first black man to win the Congressional Medal of Honor. Lincoln himself noted that the Union forces might have had to negotiate a peace with the Confederacy if the black soldiers had not taken part in the war effort.
Conditions for African American soldiers were poor. Until 1864, they were paid less than their white colleagues. They faced the threat of being enslaved of captured by Confederates. The capture of Fort Pillow was one incident which many feel reveals the dangers which threatened African American troops. On April 12, 1864, Confederate Gen. Nathan Bedford Forrest captured a Union post, Fort Pillow, in Tennessee. Forrest's Confederate troops killed dozens of unarmed black soldiers, as well as some white soldiers. Of the 570 troops in the fort, a little less than half were black. Of the Union troops, 231 were killed, 100 were wounded and 226 were taken prisoner, while the Confederates lost 14 dead and 86 wounded. The black troops were killed in large numbers, with only 58 out of 262 taken prisoner. Forrest reportedly explained: "it is hoped that these facts will demonstrate ... that Negro soldiers cannot cope with Southerners."

The events that took place at Fort Pillow remain in dispute. The Union claimed that a large number of Union troops were killed after they had surrendered the fort, making the Fort Pillow incident a shocking massacre. The Confederacy provided other explanations for the casualties, including the unusually high number of black casualties. Congress' Committee on the Conduct of the War investigated the incident, but evidence remains split between Union accusations and Confederate explanations. It is highly unlikely, however, that all the Union casualties at Fort Pillow were necessary for Forrest and his troops to simply take the garrison; and that the Confederate forces were entirely without malice. Whether the bulk of the casualties occurred before or after the surrender of the fort, however, has not been definitively established.

In the South, nearly everyone opposed the enlistment of African Americans. According to Georgia politician Howell Cobb, "the day you make soldiers of them is the beginning of the end of the revolution ... If slaves will make good soldiers, then our whole theory of slavery is wrong." Nevertheless, On March 15, 1865, Gen. Robert E. Lee was so desperate for soldiers that he wrote to Jefferson Davis, requesting slave troops. The slaves would be promised freedom at the end of the war. Although the Confederate Congress then authorized the enlistment of slaves, allowing the states to determine their policies; few African American soldiers fought for the Confederacy.