After the start of
World War II in 1939, Capesius joined the
Romanian army and rose to the rank of captain while serving at a military hospital's pharmacy. In January 1942, for reasons not made clear in his military records, he was granted leave to restart his civilian job as a national sale representative for
IG Farben and
Bayer. He traveled so much that at times he lived in both Klausenburg and Sighisoara before finally buying a sixth-floor condominium on Brezoianu Street in an upper-class Bucharest neighborhood. He moved his family there. After training at the
SS-Zentrale Sanitäranlage (Central Sanitary Facility) in Warsaw, he was sent to
Dachau Concentration Camp in September 1943; he worked there until his subsequent transfer to
Auschwitz Concentration Camp in December 1943. In Auschwitz, he acted as the chief KZ-Apotheker (pharmacist) starting in February 1944 after his predecessor was executed for "spreading defeatism." Capesius worked closely with
Josef Mengele and together they were heavily involved in the selection of inmates for the gas chamber beginning in the spring of 1944 when the Hungarian and Transylvanian Jews were sent to the camp. He was the only SS selector who was recognized at the arrival ramp by Jews who had known him personally or through his pharmaceutical work before the war. In Auschwitz, he had risen to the rank of
SS-Sturmbannführer, in November 1944, and was in charge and control of the poisonous chemicals used in the extermination of the Jews, such as
phenol and
Zyklon B. This was during the mass murder of almost 400,000 Hungarian Jews. During his time at Auschwitz, Capesius stole valuables from the personal belongings of arriving Jews at the railhead and also secreted away gold pulled from the dental fillings of corpses. He had access to the gold since it was under the control of the camp's dentists, with whom he shared his pharmaceutical dispensary. Capesius sent the stolen gold to his sister for safekeeping until after the war. ==Post-War==