Guerrilla warfare is generally defined as irregular warfare,in which persons engaged in an action do not operate under command of the regular army. Such independent activity can be authorized,as when the Confederate Congress ordained partisan units to operate behind Union lines, or it can be spontaneous acts of sabotage and harassment.

Revolutionary War heroes like Francis Marion, Thomas Sumter, and "Light Horse" Harry Lee gave Southerners a tradition of guerrilla fighting long before the start of the Civil War, and partisan warfare naturally became a part of their own struggle for independence. The first guerrilla action of the war occurred in April 1861, when Baltimore mobs attacked Northern troops passing through the city. Secessionist guerrillas also cut telegraph communications, burned bridges, and tore up railroad tracks, effectively isolating Washington from the North.

The Union took control of Western Virginia early in the war, but there were enough secessionists in the population to resist the occupation. "There is not a county in all this part of the Old Dominion that does not contain a greater or less number of Secessionists, who have degenerated into assassins," wrote a Northern reporter in late summer 1861. "They are committing murders daily." A Unionist antiguerrilla guerrilla force that called itself "The Snake-Hunters" was organized from this area of Virginia to combat the Rebel Guerrillas. The two sides fought each other throughout the war.

The people of Missouri were also deeply divided in their loyalities, and the guerrilla warfare that had been carried on for years between "Jayhawkers" and "Border Ruffians" continued into the war and long after. During the fall of 1861, guerrillas operating under Col. M. Jeff Thompson, "The Swamp Fox of the Confederacy," sabotaged a bridge over the Platte River so that it collapsed under a train. On December 22, Secretary of War Henry Halleck ordered all captured guerrillas to be "immediately shot."

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