With the outbreak of the American Civil War in 1861, Le Gendre helped recruit the 51st New York Volunteer Infantry; he was commissioned a major of that regiment on October 29, 1861. Le Gendre participated in combat in North Carolina and was present at the capture of Roanoke Island in 1862. However, he was badly wounded at the Battle of New Bern, North Carolina, on March 14, 1862. He later received a citation for his courage.