Deportations on this scale required the coordination of numerous German government ministries and state organizations, including the Reich Security Main Office (RSHA), the Transport Ministry, and the Foreign Office. The RSHA coordinated and directed the deportations; the Transport Ministry organized train schedules; and the Foreign Office negotiated with German-allied states about handing over their Jews.

The Germans used both freight and passenger cars for the deportations. They did not provide the deportees with food or water, even when the transports had to wait days on railroad spurs for other trains to pass. The people deported in sealed freight cars suffered from intense heat in summer, freezing temperatures in winter, and the stench of urine and excrement. Aside from a bucket, there were no provisions for sanitary requirements. Without food or water, many deportees died before the trains reached their destinations. Armed guards shot anyone trying to escape. Between the fall of 1941 and the fall of 1944, millions of people were transported by rail to the extermination camps and other killing sites in occupied Poland and the occupied Soviet Union.