He was admitted to the bar in 1860, and had just begun the practice of his profession at Concord when the war broke out. Throwing aside his law-books, he took up the study of military tactics, joined a company then forming at Concord, under the first call for troops,--volunteering as a private, but when it came to organization was chosen captain,--and finding the quota of New Hampshire full under the first call, immediately volunteered, with a large number of his men, for three years or the war, under the second call. Recruiting his company to the maximum, he joined the Second Regiment at Portsmouth, was mustered into the United States service in June, 1861, and commanded his company at the first battle of Bull Run, handling it with coolness and bravery, although it was under a sharp fire, and lost twelve men, killed and wounded. It was the celebrated "Goodwin Rifles," Co. B, 2d N. H. Vols., armed with Sharp's rifles, by the exertions of Capt. Griffin and his friends,--the only company sent from the state armed with breech-loaders. In 1861 he was promoted to be lieutenant-colonel of the 6th N. H. Vols., and joined that regiment at its rendezvous in Keene. The regiment was assigned to Burnside's expedition to North Carolina, and landed at Hatteras island in January, 1862. In March it removed to Roanoke island, and on the 7th of April, Lieut.-Col. Griffin was sent in command of an expedition, composed of six hundred men with five gunboats, to break up a rebel rendezvous near Elizabeth City, N. C. Landing at daybreak the next morning, he attacked and broke up the camp, capturing seventy-four prisoners, three hundred and fifty stands of arms, and a quantity of ammunition. On the 19th of April, at the battle of Camden, N. C., he commanded his regiment, which formed the reserve. At the critical moment he moved it forward in line of battle, within short musket range, halted the line, gave the command to fire, and the regiment poured in a volley with wonderful coolness and precision. The enemy broke and fled, and the battle was won. On the 22d of April, 1862, he was commissioned colonel of the regiment. Assigned to Reno's division, which was sent to aid Pope in Virginia, he commanded his regiment at the second Bull Run, where it was ordered, with its brigade, to attack the enemy in a piece of wood. Forcing their way for some distance, they received a murderous fire in front and from the left flank and rear. Thinking it must be friends firing into them by mistake, Col. Griffin took the colors and waved them in that direction, but the fire only came the sharper; and finding himself nearly surrounded by an immense force, and deserted by the other regiments, he gave the order to retreat, and brought off the remnant of his men, bearing the colors himself.