Rabies in European bats was first reported in Germany in 1954. In concordance with Denmark and the Netherlands, Germany has reported one of the highest numbers (n = 187) of European bat lyssavirus (EBLV)-positive cases in bats in Europe so far (1954-2005). A combined descriptive epidemiological and phylogenetic analysis on bat rabies and prevailing EBLVs is presented, comprising the past 50 years. So far, only the two lineages of EBLV-1 (genotype 5), a and b, have been detected. Although only 50% of the rabies-positive bats have been identified by species, the Serotine bat (Eptesicus serotinus) is the bat species most frequently infected. Single rabies cases have also been detected in a further five indigenous bat species. There is proven evidence for a substantial bias in the frequency of bat rabies cases in the north of Germany, with an endemic cluster in the northwesternmost low-lying plain areas adjacent to the Netherlands and Denmark. Improvements to bat rabies surveillance and research are discussed.