[2] At the outbreak of the Civil War, Patterson rejoined the army and was commissioned colonel of the 17th Pennsylvania Volunteer Infantry, a ninety-day militia regiment which saw service as guard duty along the Potomac River.

He was promoted to brigadier general in the United States Volunteers effective April 11, 1862, and placed in command of the 3rd Brigade, 2nd Division, III Corps, Army of the Potomac.

[1] Patterson led his brigade at Williamsburg and Seven Pines, but during the latter battle, he had to relinquish command due to illness with typhoid fever.

Patterson was at Catlett's Station when he withdrew his brigade based on unconfirmed reports of Confederate troops nearby.

Sickles accused him of retreating without orders and called for a military board of inquiry to court-martial him.