Bats are the second largest mammalian population in the order Chiroptera with 18 families and approx. 1200 species. They have unique biological, physiological, and ethological features that make them ideal reservoir hosts for viruses. For instance, they live all over the world and their ability to fly enable virus spreading over long distances. The bat-associated virus database currently contains 9820 viruses from 28 families. Many of the detected viruses are with zoonotic potential in humans and domestic animals, including rabies virus, Ebola virus, Marburg virus, dengue virus and SARS coronavirus. While the virome composition of bats from several different countries such as China, Japan and the USA has been determined, no such data exists for Switzerland. In order to determine the virome of selected bat species living in Switzerland, a collaboration with Emergency Care Center for Bats (Zurich animal protection department and Zurich Zoo) and the Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich has been established.