We reviewed topographical homologies in the upper tooth morphology of bats and analyzed the implications to relationships among higher taxa within Chiroptera. A standardized terminology for the upper molars of bats is proposed, taking into consideration the nomenclature adopted for tribosphenic mammals. Major patterns of variation in crown morphology of chiropteran upper molars were reevaluated, and 2 new structures were identified: mesoconule and mesoconule crista. The main controversies in the literature regarding terminology and structural identity in the upper molars of chiropterans are discussed. Forty-eight dental morphological characters are presented for extant bats and the extinct Icaronycteridae, with the exception of Pteropodidae, which has lost the tribosphenic dental pattern. These were combined with 191 characters of other morphological systems from the literature. The tree obtained from parsimony analyses mostly agrees with previous proposals based on morphology. However, major differences were found: the position of Noctilionoidea at the base of the radiation of modern microchiropterans, which formed a trichotomy with Yinochiroptera (including Emballonuridae) and the remaining Yangochiroptera; Antrozoinae disassociated from the other Vespertilionidae, forming a poorly supported clade with Mystacinidae and Molossidae; and the relationship between the sister taxa Myotinae and Miniopterinae within Vespertilionidae.