Prisoners assigned to a Kommando employed in places of mass extermination could not refuse to do their work or ask to be transferred to perform other tasks in the camp. Failure to carry out the instructions of the SS would result in immediate death. Awareness of this fact meant that cases of prisoners refusing to burn corpses were exceedingly rare.

The personal cards of Sonderkommando prisoners were held by the concentration camp Gestapo, called the Political Department. Sonderkommando prisoners were treated as Geheimnisträger (bearers of secrets) and therefore their documents were extremely hard to find among camp records after the war.

Sonderkommando prisoners were also physically separated from other camp inmates, living in a secluded barracks with a courtyard surrounded by a wall. Originally this was barracks 2 in Birkenau sector BIb, and then, from mid-1943, it was barracks 13 in sector BIId. In the summer of 1944, as a result of the increased number of transports for the gas chambers and also due to suspicions that they were planning a revolt, Sonderkommando prisoners were quartered in the attics of crematoria II and III and in the undressing room of the then inactive crematorium IV.

The number of Sonderkommando prisoners fluctuated, depending on the intensity of mass extermination operations and the number of active mass extermination sites. In 1942 and 1943 the Sonderkommando included around 400 prisoners. Following selections at the beginning of 1944, the number fell to approximately 200 prisoners, but in the summer, it rose to 870 prisoners. This reflected intensification of mass murder in mid-1944, mostly because of the deportation of Hungarian Jews. In that time several thousand Hungarian Jews arrived almost every day.