On May 28, 1861, he was appointed an Assistant Surgeon in the U.S. Army, and on July 21 of the same year was captured at the First Battle of Bull Run, while serving with General George Sykes' division. He managed to escape and soon joined his command in the defense of Washington. He later participated in the Peninsular campaign and saw service in the battles of Gaines' Mill and Malvern Hill. During this campaign he contracted typhoid fever while at Harrison's Landing and was sent north on a transport. During the remainder of the war he performed hospital duty, mostly at Lovell Hospital at Portsmouth, Rhode Island, and at Cleveland, Ohio. On March 13, 1865, he was given the Brevets of captain and major for faithful and meritorious service.