Zündel was born in Calmbach (now part of Bad Wildbad) in Baden-Württemberg, Germany in 1939 and was raised mostly by his mother, Gertrude. His father, Fritz, a lumberjack, was drafted into the German Army shortly after Ernst's birth and served as a medic on the Eastern Front. His father was captured and incarcerated as a prisoner of war and did not return home until 1947, by which time he had become an alcoholic. Ernst was the fourth in a family of six children consisting of a brother, who later became an attorney in the United States, and four sisters.