He then became an assistant at the Physics Institute. Czerny attracted attention at the time when, following the Stern-Gerlach experiment (1922), which demonstrated the existence of half-integer quantum numbers in electron spin, he also found them in the rotation bands of molecules (gaseous hydrogen halides). His subsequent study of the rotation bands on alkali halide crystals (with R. Bowling Barnes, C. H. Cartwright) provided the first evidence of what were later described as multiphonon effects.
In 1927 he earned his habilitation and in 1934 he became an associate professor in Berlin (as the successor Peter Pringsheim, who was dismissed by the Nazi regime), but left after the institute in Berlin was switched to military research due to the change in leadership from Walther Nernst to Erich Schumann and the scientific environment deteriorated due to confidentiality regulations.
In 1938 he became a professor for experimental physics to Frankfurt and became director of the physical institute there. His predecessor Karl Wilhelm Meissner, who wanted to bring Czerny to Frankfurt in 1934, had previously been dismissed there by the National Socialists. Initially, Czerny had to pay for the equipment for infrared spectroscopy out of his own pocket, since the institute in Frankfurt had previously operated optical spectroscopy. During the Second World War, his institute was largely destroyed by bombing raids. After the war, in 1947, he spent six months in military research for the US Navy in California. After the war he led the slow reconstruction of the Physics Institute and retired in 1961. However, Czerny worked until 1976 in the internship for beginners.
In 1966 he received an honorary doctorate in Göttingen.