The aquaporins (AQPs) are a family of homologous water channels expressed in many tissues. In this study, the expression and immunolocalization of different AQP subtypes in rat brains were investigated by RT-PCR, immunohistochemistry and immunofluorescence. The data showed that AQP1 was expressed in the subpial processes of astrocytes, choroid plexus and ependyma. AQP3, AQP5 and AQP8 had similar distribution patterns in piriform cortex, choroid plexus, hippocampus and dorsal thalamus. AQP4 and AQP9 were widely expressed in the rat brain and distributed in the subpial processes of astrocytes, ependyma, dorsal thalamus, hippocampus, white matter, suprachiasmatic nucleus (SCN) and supraoptic nucleus. AQP3, AQP4, AQP5, AQP8 and AQP9 were found in the Bergmann glial cells of cerebellum, cochlear nucleus and trapezoid nuclei. The distinct localization of various AQPs in cerebrum and the similarities of distribution patterns within cerebellum, cochlear nucleus and trapezoid nuclei suggest that AQPs may play an important role in maintaining the specific microenvironments of the brain. © 2011 Blackwell Verlag GmbH.