The gain or loss of anatomical features is an important mechanism of morphological evolution and ecological adaptation. Dental anomalies—the loss or gain of teeth—are widespread and a potential source of craniodental specialization among mammals, yet their macroevolutionary patterns have been rarely explored. We present the first phylogenetic comparative study of dental anomalies across the second largest mammal Order, Chiroptera (bats). We conducted an extensive literature review and surveyed a large sample of museum specimens to analyze the types and prevalence of dental anomalies across bats, and performed phylogenetic comparative analyses to investigate the role of phylogenetic history and dietary specialization on incidence of dental anomalies. We found dental anomalies have a significant phylogenetic signal, suggesting they are not simply the result of idiosyncratic mutations or random developmental disorders, but may have ancestral genetic origins or result from shared developmental pathways among closely related species. The incidence of dental anomalies was not associated with diet categories, suggesting no effect of craniodental specialization on dental anomalies across bats. Our results give insight into the macroevolutionary patterns of dental anomalies in bats, and provide a foundation for investigating new hypotheses underlying the evolution of dental variation and diversity in mammals.