Whitside next served as an aide-de-camp on the staff of Major General Nathaniel Banks, and participated in the Siege of Port Hudson in Louisiana in 1863. However, Whitside suffered from a number of ailments—including smallpox—and was severely injured at the Battle of Culpeper Court House. After briefly serving as an aide to generals John H. Martindale and Alfred Pleasonton, he spent the remainder of the Civil War on recruiting duty in Rhode Island and mustering duty in West Virginia. He later received brevet promotions to captain and major for faithful and meritorious service.