Borneo has a significant role to play in the conservation of bat diversity in Southeast Asia, yet there is little taxonomic and distribution information available for the Indonesian states that represent over two thirds of the island. We report the results of a four week harp-trap and mistnet survey of four limestone karst formations on the Sangkulirang peninsula in East Kalimantan during August 2004. We recorded 36 taxa, including two (a Pipistrellus and Rhinolophus) that may represent new species, and three (Hipposideros bicolor, Myotis horsfieldii and M. montivagus) that are new records for Kalimantan. Several species, including the karst dependent and patchily distributed Hipposideros larvatus, Rhinolophus creaghi and R. pusillus, were highly abundant at the formations. In Borneo, many of the species were previously known from only a few, or scattered, localities including four Red-Listed species (R. creaghi, M. montivagus, Murina rozendaali and Kerivoula minuta). We review the Bornean distributions of individual species given recent surveys in Kalimantan and present taxonomic data from 135 specimens collected during this study. This represents the largest bat collection in Kalimantan so far undertaken and highlights the Sangkulirang peninsula as a key site for bat diversity and conservation in Borneo. Threats to this area include disturbance from bird nest collection in caves, but also mass disturbance from logging and forest fires. We advocate inclusion of the formations and associated forests into a protected area to safeguard this biological resource.