After the outbreak of the war and through the summer of 1861, Smith served on recruiting duty as commander of Fort Columbus, New York. He was commissioned a brigadier general of volunteers, and as colonel in the Regular Army, commanding the 3rd U.S. Infantry regiment, as of September 9. He was soon transferred to the Western Theater to command the District of Western Kentucky. He then became a division commander in the Department of the Missouri under Brigadier General Ulysses S. Grant, who had been one of his pupils at West Point. This potentially awkward situation was eased by Smith's loyalty to his young chief. The old soldier led his division of raw volunteers with success at the Battle of Fort Donelson in February 1862. During the attack on the Confederate right flank, which he led personally, he saw some of his men waver. He yelled to them, "Damn you gentlemen, I see skulkers, I'll have none here. Come on, you volunteers, come on. You volunteered to be killed for love of country, and now you can be. You are only damned volunteers. I'm only a soldier, and don't want to be killed, but you came to be killed and now you can be." Smith's experience, dignity, and unselfish character made him Grant's mainstay in the early days of the war. When theater commander Major GeneralHenry Halleck became distrustful and perhaps jealous of Grant, he briefly relieved him of field command of the Army's expedition up the Tennessee River toward Corinth, Mississippi and gave that responsibility to Smith. However, Halleck soon restored Grant to field command. Grant's restoration was fortunate because by the time Grant reached Savannah, Tennessee, Smith had already met with an accident while jumping into a rowboat that seriously injured his leg, forcing him out of field duty. His senior brigadier, W.H.L. Wallace, led his division at the Battle of Shiloh.
Death
Smith died of an infection following his foot injury and chronic dysentery at Savannah, Tennessee, and was buried in Laurel Hill Cemetery in Philadelphia. The early close of his career in high command deprived the Unionarmy of one of its best leaders, and his absence was nowhere more felt than on the battlefield of Shiloh, where the Federals paid heavily for the inexperience of their generals. A month before his death, he had been made major general of volunteers. Two forts were named in his honor. The first Fort C. F. Smith was part of the perimeter defenses of Washington, D.C. during the American Civil War. A second Fort C. F. Smith was located at the Bighorn River crossing of the Bozeman Trail in the Montana Territory during Red Cloud's War.