Since 1994, a number of novel viruses have been described from bats in Australia and Malaysia, particularly from fruit bats belonging to the genus Pteropus (flying foxes), and it is probable that related viruses will be found in other countries across the geographical range of other members of the genus. These viruses include Hendra and Nipah viruses, members of a new genus, Henipaviruses, within the family Paramyxoviridae; Menangle and Tioman viruses, new members of the Rubulavirus genus within the Paramyxoviridae; and Australian bat lyssavirus (ABLV), a member of the Lyssavirus genus in the family Rhabdoviridae. All but Tioman virus are known to be associated with human and/or livestock diseases. The isolation, disease associations and biological properties of the viruses are described, and are used as the basis for developing management strategies for disease prevention or control. These strategies are directed largely at disease minimization through good farm management practices, reducing the potential for exposure to flying foxes, and better disease recognition and diagnosis, and for ABLV specifically, the use of rabies vaccine for pre- and post-exposure prophylaxis. Finally, an intriguing and long-term strategy is that of wildlife immunization through plant-derived vaccination.