Following the end of the war and obtaining his PhD in physical chemistry from Carnegie Tech, Cowan returned to work for Los Alamos in 1950. Only weeks after his arrival, he directed the detection of radioactive fallout from samples collected near the Russian border indicating the Soviets were in possession of a nuclear bomb. He also participated for some years in the Bethe Panel, whose first chairman was Hans Bethe. One of his early participatory functions on the panel was to convince U.S. government officials that the radiochemistry of the samples proved that it was not the result of a peaceful nuclear reactor problem, but a Soviet bomb, which was dubbed "Joe-1" after Joseph Stalin.