With more than 1 200 species, bats and flying foxes (Order Chiroptera) constitute the most important and diverse order of Mammals after Rodents. Many species of bats are insectivorous while others are frugivorous and few of them are hematophagous. Some of these animals fly during the night, others are crepuscular or diurnal. Some fly long distances during seasonal migrations. Many species are colonial cave-dwelling, living in a rather small home range while others are relatively solitary. However, in spite of the importance of bats for terrestrial biotic communities and ecosystem ecology, the diversity in their biology and lifestyles remain poorly known and underappreciated. More than sixty viruses have been detected or isolated in bats; these animals are therefore involved in the natural cycles of many of them. This is the case, for instance, of rabies virus and other Lyssavirus (Family Rhabdoviridae), Nipah and Hendra viruses (Paramyxoviridae), Ebola and Marburg viruses (Filoviridae), SARS-CoV and MERS-CoV (Coronaviridae). For these zoonotic viruses, a number of bat species are considered as important reservoir hosts, efficient disseminators or even directly responsible of the transmission. Some of these bat-borne viruses cause highly pathogenic diseases while others are of potential significance for humans and domestic or wild animals; so, bats are an important risk in human and animal public health. Moreover, some groups of viruses developed through different phylogenetic mechanisms of coevolution between viruses and bats. The fact that most of these viral infections are asymptomatic in bats has been observed since a long time but the mechanisms of the viral persistence are not clearly understood. The various bioecology of the different bat populations allows exchange of virus between migrating and non-migrating conspecific species. For a better understanding of the role of bats in the circulation of these viral zoonoses, epidemiologists must pay attention to some of their biologic properties which are not fully documented, like their extreme longevity, their diet, the population size and the particular densities observed in species with crowded roosting behavior, the population structure and migrations, the hibernation permitting overwintering of viruses, their particular innate and acquired immune response, probably related at least partially to their ability to fly, allowing persistent virus infections and preventing immunopathological consequences, etc. It is also necessary to get a better knowledge of the interactions between bats and ecologic changes induced by man and to attentively follow bat populations and their viruses through surveillance networks involving human and veterinary physicians, specialists of wild fauna, ecologists, etc. in order to understand the mechanisms of disease emergence, to try to foresee and, perhaps, to prevent viral emergences beforehand. Finally, a more fundamental research about immune mechanisms developed in viral infections is essential to reveal the reasons why Chiroptera are so efficient reservoir hosts. Clearly, a great deal of additional work is needed to document the roles of bats in the natural history of viruses.