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He completed his medical doctorate on 22 March 1922 and received his medical license. After two years of clinical training, he opened a practice in Komotau, specializing in skin and sexually transmitted diseases. His application to join the Nazi party was declined in 1939, because he had been married to a Jewish physician from whom he had been divorced in April 1935.
During World War II, Pokorny worked as a medical officer of the German Armed Forces. Pokorny, an admirer of Heinrich Himmler, wrote to Himmler to support his decision to sterilize Jewish prisoners of war. Pokorny wrote to advise Himmler to use the sap of a caladium plant, which caused sterilization in males and females. This method was later used to sterilize thousands of women in Auschwitz. Pokorny was tried by the American Military Tribunal No. I (also known as the Doctors' Trial) in August 1947. However, he was acquitted of having participated in compulsory sterilization experiments.
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