The Institute of Environmental Medicine (IEM) is closely connected with scientists from Greater Munich, especially from the Technical University of Munich (TUM), the Helmholtz Zentrum München - German Research Center for Environmental Health (HMGU), the Ludwig-Maximilians-Universität Munich (LMU), and finally the School of Life Sciences Weihenstephan (WZW).

An additional collaboration consists together with the Helmholtz Zentrum München via the Cooperative Health Research in the Augsburg Region (KORA-Studies), by which the IEM constantly receives important research data, and via the National Cohort (NaKo). Within the field of Environment and Health Sciences, the IEM has close connections to environmental researchers from the University of Augsburg. Besides the research laboratory at the HMGU, there exists another research laboratory on the campus of the Klinikum Augsburg, which forms the nucleus of the Translational Research Center (TRC) together with the Outpatient Clinic for Environmental Medicine (Ambulanz für Umweltmedizin am Klinikum Augsburg).

A special cornerstone of research and education within the field of allergology is the international consortium project CK-CARE - Christine Kühne Center for Allergy Research and Education, Davos. Another important collaborationist of the IEM is the Environmental Research Station Schneefernerhaus - Zentrum für Höhen- und Klimaforschung, by which help important data for current environmental research is made available. An additional support comes from the Bavarian State Department for Environment (LfU), which has a cutting edge pollen monitor on its site, which is run as an interdisciplinary project of UNIKA-T.

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