As Germany conquered much of Europe in the years 1939-1941, the SS established a number of new concentration camps to incarcerate increased numbers of political prisoners, resistance groups, and groups deemed racially inferior, such as Jews and Roma (Gypsies). Among these new camps were: Gusen (1939), Neuengamme (1940), Gross-Rosen (1940), Auschwitz (1940), Natzweiler (1940) Stutthof (1942), and Majdanek (February 1943). Stutthof had been a Gestapo Labor Education camp from 1939 to 1942.

After the beginning of the war, the concentration camps also became sites for the mass murder of small targeted groups deemed dangerous for political or racial reasons by the Nazi authorities. For example, several hundred Dutch Jews were rounded up in retaliation for a Dutch transit strike in protest of Nazi persecution of Jews in the Netherlands in the winter of 1941. They were sent to Mauthausen in February 1941 where within a few days, the SS staff had killed all of them. Thousands of "security suspects" released from German prisons in the autumn of 1942 were sent to concentration camps and literally worked to death under a program called "Annihilation through Work" (Vernichtung durch Arbeit). Finally, captured members of national resistance movements were sent to concentration camps to be murdered upon arrival.