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We assessed injuries to the forearms of 17 species of microchiropteran bats marked for ecological studies and banded under the auspices of the Australian Bird & Bat Banding Scheme. Serious injuries were recorded in 16 of the 17 species, but injury rates varied between species according to band type, band size and metal type. Survival estimates were calculated for three species. In Nyctophilus geoffroyi mean annual survival was significantly lower for animals marked with bat bands that caused major injuries to 7.1% of recaptured animals than that for animals marked with bird bands that produced negligible injury rates. The results of this study have led the Australian Bird & Bat Banding Scheme to adopt a precautionary principle and impose a moratorium on the banding of bats belonging to the families Vespertilionidae, Molossidae and Emballonuridae. Applications to band microchiropteran bats are now considered on a case-by-case basis. Rigorous trials on target species are required to evaluate the efficacy of the marking technique proposed before banding approval is granted. Banding of potentially sensitive species is limited to studies in which the impacts of banding can be evaluated directly, such as at known roost sites. There is a need to develop alternative methods for marking insectivorous bats for ecological studies of wild populations.