The Sixth Infantry was organized at Camp Randall, Madison, WI and mustered into the service of the United States on July 16, 1861. The regiment left the state on July 28, reaching Washington, D.C., August 7, 1861, and going into camp in the suburbs of that city. Shortly thereafter the Sixth was attached to General King's Brigade, which subsequently became known as the "Iron Brigade". From that time until March 1862, the regiment served in the defenses of Washington, and thereafter in all the campaigns of the Army of the Potomac except the Peninsular Campaign until the surrender at Appomattox.

In March, 1862, the First Corps was organized and the Iron Brigade assigned thereto. With this Corps the regiment and the Second and Seventh Infantry served until March, 1864, when the organization was discontinued, and the Iron Brigade transferred to the Fifth Corps, with which it was subsequently identified. The Sixth took part in the Grand Review at Washington, and shortly thereafter was, with other regiments of the Army of the Potomac, transferred to Louisville, KY, where it was mustered out of the service of the United States July 14, 1865, and disbanded at Madison July 16, 1865.