Robert E. Lee's Army of Northern Virginia—about 55,000 men^[1] — entered the state of Maryland on September 3, following their victory at Second Bull Run on August 30. Emboldened by success, the Confederate leadership intended to take the war into enemy territory. Lee's invasion of Maryland was intended to run simultaneously with an invasion of Kentucky by the armies of Braxton Bragg and Edmund Kirby Smith. It was also necessary for logistical reasons, as northern Virginia's farms had been stripped bare of food. Based on events such as the Baltimore riots in the spring of 1861 and the fact that President Lincoln had to pass through the city in disguise en route to his inauguration, Confederate leaders assumed that Maryland would welcome the Confederate forces warmly. They sang the tune "Maryland, My Maryland!" as they marched, but by the fall of 1862 pro-Union sentiment was winning out, especially in the western parts of the state. Civilians generally hid inside their houses as Lee's army passed through their towns, or watched in cold silence, while the Army of the Potomac was cheered and encouraged. Some Confederate politicians, including President Jefferson Davis, believed that the prospect of foreign recognition would increase if the Confederacy won a military victory on Union soil; such a victory might gain recognition and financial support from the United Kingdom and France, although there is no evidence that Lee thought the Confederacy should base its military plans on this possibility.^[2]

While McClellan's 87,000-man^[3] Army of the Potomac was moving to intercept Lee, two Union soldiers (Cpl. Barton W. Mitchell and First Sergeant John M. Bloss^[4] of the 27th Indiana Volunteer Infantry) discovered a mislaid copy of Lee's detailed battle plans — Special Order 191 — wrapped around three cigars. The order indicated that Lee had divided his army and dispersed portions geographically (to Harpers Ferry, West Virginia, and Hagerstown, Maryland), thus making each subject to isolation and defeat if McClellan could move quickly enough. McClellan waited about 18 hours before deciding to take advantage of this intelligence and reposition his forces, thus squandering an opportunity to defeat Lee decisively.^[5]

There were two significant engagements in the Maryland campaign prior to the major battle of Antietam: Maj. Gen. Thomas J. "Stonewall" Jackson's capture of Harpers Ferry and McClellan's assault through the Blue Ridge Mountains in the Battle of South Mountain. The former was significant because a large portion of Lee's army was absent from the start of the battle of Antietam, attending to the surrender of the Union garrison; the latter because stout Confederate defenses at two passes through the mountains delayed McClellan's advance enough for Lee to concentrate the remainder of his army at Sharpsburg.^[6]