In the 1862 Peninsula Campaign, Warren commanded his regiment at the Siege of Yorktown and also assisted the chief topographical engineer of the Army of the Potomac, Brig. Gen. Andrew A. Humphreys, by leading reconnaissance missions and drawing detailed maps of appropriate routes for the army in its advance up the Virginia Peninsula. He commanded a small brigade (3rd Brigade, 2nd Division, V Corps) during the Seven Days Battles consisting of his own 5th New York along with the 10th New York. At Gaines Mill, he was bruised in the knee by a shell fragment, but remained on the field. He continued to lead the brigade at the Second Battle of Bull Run, suffering heavy casualties in a heroic stand against an overwhelming enemy assault, and at Antietam, where the V Corps was in reserve and saw no combat.