From 1942 to 1945, Schilling's research on malaria and attempts at fighting it using synthetic drugs culminated in human experimentation on over a thousand camp prisoners at Dachau, of whom hundreds died.

Upon retirement from the Robert Koch Institute in 1936, Schilling moved to Benito Mussolini's Fascist Italy, where he was given the opportunity to conduct immunization experiments on inmates of the psychiatric asylums of Volterra and San Niccolò di Siena.

As Schilling stressed the significance of the research for German interests, the Nazi government of Germany also supported him with a financial grant for his Italian experimentation.

[2] Schilling returned to Germany after a meeting with Leonardo Conti, the Nazis' Health Chief, in 1941, and by early 1942 he was provided with a special malaria research station at Dachau's concentration camp by Heinrich Himmler, the leader of the SS.

Of the more than 1,000 prisoners used in the malaria experiments at Dachau during the war, between 300 and 400 died as a result; among survivors, a substantial number remained permanently injured.

[2] In the course of the Dachau Trials following the liberation of the camp at the close of the war, Schilling was tried by a U.S. General Military Court, appointed at 2 November 1945, in the case of The United States versus Martin Gottfried Weiss, Wilhelm Rupert, et al.

Breaking down in tears at the end, he pleaded with the court to let him finish his research, albeit in a less destructive manner:"I have worked out this great labor.