Between 1933 and 1945, the Robert Koch Institute was closely involved in the National Socialist policy of violence as a public health research institution. From 2006 to 2008, historians from the Institute for the History of Medicine at the Charité in Berlin researched the role of the RKI under National Socialism. The aim of the project, which was initiated and financed by the RKI, was to examine the scientific, political and science policy activities of the RKI during this period as comprehensively as possible and without institutional bias. The results were published in the book "The Robert Koch Institute under National Socialism" (in German). Since 2011, an artistic memorial at the RKI has helped to keep the debate on the topic alive.

Several scientists and assistants had to leave the institute in the spring of 1933 because of their Jewish background. In 2021, the RKI museum team dedicated a separate podcast episode to each of the twelve former Jewish employees in the podcast "Remembering" to honour their achievements and remember their fate.