Patterson led his brigade at Williamsburg and Seven Pines, but during the latter battle, he had to relinquish command due to illness, apparently typhoid fever. He took a leave of absence on June 7 and so missed the Seven Days Battles entirely. By July, he was well enough to take on administrative duties at army headquarters. Patterson did not return to field command until the fall months when he resumed command of his old brigade, now in Daniel Sickles's division. However, recurrent ill health continued to plague him.