We examined 686 skulls of 420 species of microchiropteran bats in 16 families to assess variation in pits in the basisphenoid and basioccipital bones. A total of 26 measurements were used to describe variation in pits, and patterns in the distribution of pits were examined across the families. Pits were absent from 154 species and present in 266 species. While some species had as many as four basisphenoid pits, basioccipital pits, when present, always occurred as a single pair. No species had more than four pits (basisphenoid or basioccipital and basisphenoid) in total. In some families all species either had pits (e.g. Emballonuridae) or none had pits (e.g. Rhinolophidae), but the incidence of pits usually was variable within families. The results of a cluster analysis of families based on the incidence of pits and morphological features of pits bore little resemblance to a recent phylogeny of Microchiroptera. A discriminant function analysis of features of pits of Emballonuridae, Phyllostomidae, Vespertilionidae and Molossidae correctly classified 66% of species to family revealing some continuity in pit structure among related species. There was no evidence of significant sexual dimorphism in the incidence or features of pits. Basisphenoid and basioccipital pits tended to increase in size with skull size. Neither the incidence nor the morphology of basisphenoid nor basioccipital pits was consistently associated with echolocation, diet or foraging behaviour. Pits were present or absent from species using either high-intensity or low-intensity echolocation calls, and the same was true of bats using high or low duty cycle modes of echolocation. Furthermore, the presence or absence of pits did not correspond to the presence or absence of harmonics in echolocation calls. We propose that basisphenoid and basioccipital pits are oscillators in the vocal tract and contribute to the production of non-linear phenomena in vocalizations made by bats. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 78, 215–233.