Born in Karlsruhe, Germany, Fischer joined the Nazi party soon after it was established. A book, Human Hereditary Teaching and Racial Hygiene, co-written by him and Edwin Bauer and Fritz Lentz, served as the "scientific" basis for Nazism's attitude toward other races. He served as the head of the Kaiser Wilhelm Institute of Anthropology, Human Heredity, and Eugenics, until 1933, when Hitler appointed him rector of the University of Berlin.
Under the Nazi regime, Fischer developed the physiological specifications used to determine racial origins. He and his team experimented with Gypsies and African-Germans, taking blood and measuring skulls to find scientific validation for his theories.
Fischer retired from the university in 1942. After the war, he completed his memoirs, which critics say whitewash his role in the genocidal program of the Third Reich. He died in 1967.