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He completed his medical doctorate on March 22, 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 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.