In 1941, in the midst of World War II, Prelog was invited to lecture in Germany by Richard Kuhn. Shortly afterwards, Lavoslav Ružička, whom Prelog asked for help, invited Prelog to visit him on his way to Germany. He and his wife used those invitations to escape to Zürich in Switzerland. With Ružičkas help, he gained support from CIBA Ltd. and started to work in the Organic Chemistry Laboratory in the Swiss Federal Institute of Technology (ETH, or Eidgenössische Technische Hochschule). Prelog was able to separate the chiral enantiomers of Trögers base in 1944 by chromatography on an optically active substrate.
With this chiral resolution, he was able to prove that not only carbon but also nitrogen atoms can be the chiral centre in a molecule, which had been speculated for several years. His relationship with Ružička helped him climb up the academic hierarchical ladder. Starting as an assistant, he became Privat-Dozent, Titularprofessor, associate professor, and in 1952 full professor. In 1957 he succeeded Ružička as head of the Laboratory. Since Prelog disliked administrative duties, he implemented rotating chairmanship in the ETH. Prelog joined the ETH at the right time, since Ružička's Jewish co-workers left the country and went to the United States, so Prelog filled the vacuum they left.