Bats are important reservoir hosts of RNA viruses, including lyssaviruses, which can cross the species barrier to infect humans and other domestic and wild non-flying mammals. Six of the seven Lyssavirus genotypes described to date infect bats. In Europe, two genotypes of Lyssavirus, European bat Lyssavirus types 1 and 2 (EBLV-1 and EBLV-2), circulate among several bat species and numerous bats are found infected every year. To provide epidemiologists and public health officials with data to effectively implement public health measures, we have undertaken field studies to identify the temporal dynamics of virus infection in bat colonies by combining multidisciplinary approaches. We have focused our work on a long-term longitudinal survey of different bat colonies in the Balearic Islands. The prevalence of virus RNA and neutralizing antibodies were analysed in captured bats. The bats were banded to allow for individual monitoring of infection and movements between colonies. The results show different lyssavirus infection episodes across the twelve years of study and provide the first evidence that mortality of the mouse-eared bat (Myotis myotis) in their natural environment does not increase significantly after episodes of EBLV-1 infection.