Miles had achieved the rank of Colonel by 1859. He was stationed at Fort Leavenworth in Kansas when the Civil War began. He was sent to Virginia and placed in command of an infantry brigade under Major general Robert Patterson. Then he was given command of a division under Brigadier general Irvin McDowell. He was at First Battle of Bull Run, but his division was held in reserve. He was then accused of being drunk at the battle. A Court of Inquiry was held and he was found guilty. A court-martial was not held. But Miles was not given another command until March 1862.