In August 1943, a gas chamber was constructed in Natzweiler-Struthof in one of the buildings that had formed part of the hotel compound. The bodies of more than 80 Jewish prisoners gassed at Natzweiler-Struthof were sent to the Strasbourg University Institute of Anatomy. There, anatomist Dr. August Hirt amassed a large collection of Jewish skeletons in order to establish Jewish "racial inferiority" by means of anthropological study. The gas chamber was also used in pseudoscientific medical experiments involving poison gas. The victims of these experiments were primarily Roma (Gypsies) who had been transferred from Auschwitz. Prisoners were also subjected to experiments involving treatment for typhus and yellow fever.

In 1944, concentration camp prisoners became increasingly important in German armaments production. The Germans used prisoners throughout the Natzweiler-Struthof camp system as forced laborers to produce arms and to construct underground manufacturing facilities. (Allied air raids on industrial complexes necessitated the construction of such facilities.)