Promoted to major in the new 16th U.S. Infantry Regiment in May 1861, he was attached to General Buell's command and took part in the Corinth campaign and the relief of Nashville. He led his battalion into the Battle of Stones River in December, receiving a wound that incapacitated him for the rest of the war. He was taken prisoner the following day but released during the Confederate retreat. In April 1863, backdated to November 29, 1862, he became brigadier general of volunteers. He served in administrative posts in Ohio and New York.