Caves are among the most important roosts of hundreds of bat species worldwide. However, caves can be formed in different lithologies. Cave structure and characteristics, which are shaped by lithology, can, in turn, influence roost preferences for different bat species. Therefore, cave lithology and characteristics can help us better understand why some bat species may be rare in some caves and common in others. Brazil is a continental country rich in bat species (182 spp.), lithologies, and caves (> 23,000). However, only a small fraction of the known caves have been sampled for bats so far, with no emphasis on the role lithology may have. Based on a literature review and using data on bat occurrence, in this study, we explore the bat species rarity in Brazilian caves and investigate the influence of lithology on bat species richness. We considered the caves' type of use (primarily, regular or occasional) that each bat species presents in the country's different biomes and the relationship between lithology and cave size. We highlight the presence of endangered species in the caves and its conservation implications.