Bayer (along with BASF and Hoechst) was an original member of the IG Farben group. During WWII, IG Farben built a synthetic rubber and oil plant complex called Monowitz close to the Auschwitz concentration camp. Inmates worked as slave labour for IG Farben, and when they were too weak to work they were killed in the gas chambers. IG Farben subsidiary Degesch manufactured Zyklon B, the gas used in the concentration camp gas chambers.

Bayer head Carl Duisberg personally propagated the concept of forced labour during WW1.The company placed itself under a large burden of guilt due to its heavy involvement in the planning, preparation and implementation of both world wars. The International War Crimes Tribunal pronounced the company guilty for its share of responsibility in the war and the crimes of the Nazi dictatorship.

On 29 July 1948, sentences for mass murder and slavery were handed down at the Nuremberg trials to twelve Farben executives. The longest sentence of only seven years was dealt out was to Dr. Fritz ter Meer, a top executive and scientist on the IG Farben managing board.

After the war, IG Farben separated into three giant corporations: Bayer, Hoechst and BASF. On 1 August 1963, Bayer celebrated its 100th anniversary at the Cologne fairgrounds. The opening speech was delivered by Dr. Fritz ter Meer, not only out of prison but - a convicted mass murderer -elevated to the position of Chairman of the Supervisory Board of Bayer.