Ulrich Hagen continued his research work as 'Privatdozent' at the Radiological Institute of the University of Freiburg, from 1961 to 1965. In 1965, he accepted an appointment at the Institute of Radiation Biology of the Kernforschungszentrum Karlsruhe (under the leadership of Karl Günter Zimmer). He remained there for 12 years studying the structure of irradiated DNA. During those years, he recognized and documented the problem of RNA polymerase inhibition by damaged DNA templates and was among the first German radiation biologists to become aware of the important role of DNA repair, as relates to endpoints: mutagenesis, aberration formation, cell death, and carcinogenesis. Ulrich Hagen became the Director of the Institute of Radiation Biology of the GSF – Gesellschaft für Strahlenforschung in Neuherberg (which was later renamed GSF – National Research Center for Environment and Health), in 1979. As the Director of Radiation Biology of the GSF, he was able to unify a number of heterogeneous radiological disciplines that had arisen at the GSF institute. In 1995, he was elected President of the 10th International Congress of Radiation Research in Würzburg, Germany and was, for 16 years, the Managing Editor of "Radiation and Environmental Biophysics", Springer-Verlag.