In May 1861 he recruited the 18th Illinois Volunteer Infantry Regiment, and was appointed as its first colonel. His time in command of the regiment in Kentucky and Tennessee was controversial and an "ordeal." He was suffered a wound during the Battle of Fort Donelson. In November 1862 he was commissioned as a brigadier general, and commanded a brigade in the Second Division of the XIII Corps. He fought with distinction in the Vicksburg Campaign in 1863. He led his men in the battles of Port Gibson, Champion's Hill, and Big Black River Bridge. and during the general assault of May 22, 1863 on Vicksburg MS, where troops under his command were the only Union forces to enter the Confederate works at the Railroad Redoubt where they planted the U.S. flag.