In 1861, Hays entered the Confederate Army as colonel of the 7th Louisiana Infantry. Showing his attitude toward Northerners, Hays made the rogue's march of his regiment "Yankee Doodle," stating that "More rascals have marched to that tune in one day than to any other." After fighting at the First Battle of Bull Run and Stonewall Jackson's Shenandoah Valley Campaign of 1862, he was shot in the shoulder and knocked unconscious by a shell burst at Port Republic.