Cowdin was colonel of the 2nd Massachusetts Militia Regiment at the start of the war, and was appointed colonel of the 1st Massachusetts Infantry on May 25, 1861. He led his regiment at the battle of Blackburn's Ford on July 18, 1861, was part of Israel B. Richardson's brigade of Daniel Tyler's Division at the First Battle of Bull Run, where his horse was killed. He also saw action at Williamsburg, Fair Oaks, Glendale, Malvern Hill and Chantilly.