Col. Corcoran was in the process of being court-martialed when the Civil War erupted. Needing as many men at arms as quickly as possible, the charges were dropped and the Army rushed the 69th to Virginia.
At the First Battle of Bull Run (First Manassas), the regiment served under the command of Colonel William T. Sherman, and was one of the few Union regiments to retain cohesion after the defeat, despite the wounding and capture of Col. Corcoran by Confederate forces. The 69th served as the Army of the Potomac's rear guard during the disorganized retreat to the defenses of Washington.
After Bull Run, Thomas Francis Meagher, the Captain of Company K, applied to have the 69th New York Volunteer Militia reorganized into Federal service as the core unit of a larger brigade composed predominantly of Irish immigrants. Meagher was promoted to brigadier general and designated the brigade's commander. Before the war, he was a leading agitator for Irish independence from Britain. A visible participant in the failed Rebellion of 1848, he was afterward tried and sentenced to death (commuted to life imprisonment in Australia, but he escaped to San Francisco CA). Gen. Meagher's battle sword, made by Tiffany & Co, is now on permanent exhibit at the Fredericksburg and Spotsylvania National Military Park
The brigade suffered its most severe casualties in December at the Battle of Fredericksburg where its fighting force was reduced from over 1600 to 256. The brigade was involved in the northern battleground at Fredericksburg where they assaulted the sunken road in front of Marye's Heights. Coincidentally, one of the regiments manning the sunken road defenses was a predominantly Irish Regiment commanded by Brigadier General Thomas Reade Rootes Cobb. Knowing that Cobb's men manned the wall, and that both Cobb's and Meagher's units contained members of the Irish Republican Brotherhood, an organization dedicated to gaining military experience in the United States, then freeing Ireland from Britain after the Civil War, Lee ordered reserves sent to the position. He need not have worried. Cobb's men helped decimate the Irish Brigade before the reinforcements could settle in place. It was at Fredericksburg that Lee allegedly referred to Meagher's regiment as the "Fighting 69th".
After the Battle of Fredericksburg, Gen. Meagher again requested to recruit the brigade back to strength. This time the request was denied. In May 1863, the brigade sustained further casualties at the Battle of Chancellorsville, Meagher repeated his request to recruit replacements, was denied, and resigned his commission in protest. Meagher was replaced by Colonel Patrick Kelly.
Leading up to the Battle of Gettysburg, the brigade recovered several hundred of its injured from Fredericksburg and was able to field nearly 600 men - in reality, barely at regimental size. At Gettysburg, the brigade distinguished itself in the Wheatfield under the command of Col. Kelly as the 2nd Brigade of the 1st Division