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When the American Civil War began, Barton resigned her position to devote herself to the care of wounded soldiers on the field of battle. In 1864 she was appointed by General Benjamin Butler "lady in charge" of the hospitals at the front of the Army of the James. In 1865 she was sent to Andersonville, Georgia, to identify and mark the graves of Union soldiers buried there. In the same year President Abraham Lincoln placed her in charge of the search for the missing men of the Union army, and while engaged in this work she traced the fate of 30,000 men.
In 1873 she inaugurated a movement to secure recognition of the Red Cross society by the United States government, which finally succeeded during the administration of President Chester A. Arthur. Barton naturally became President of the American branch of the society, which was founded in 1882. She served as president of the American Red Cross until her resignation in 1904.