The expression and localization of AQP6 were examined in rat kidneys. In the kidney compartments, the expression was more intense in the outer medulla than in the cortex or inner medulla, and was negative in the glomerulus. During development, the AQP6 mRNA expression in the kidney was not detected in the fetus, but was recognized at birth, increased gradually by 4 weeks of age, and was unchanged thereafter. In situ hybridization demonstrated significant signals for AQP6 mRNA along the outer and inner medullary collecting ducts. Since the localization of the AQP6 mRNA-expressing cells was comparable to that of immunoreactive H+ ATPase-bearing cells in the collecting duct, they were identified as intercalated cells. No AQP6 mRNA signals were recognizable in other cells in the kidneys, including glomerular cells. No glomerular expression of AQP6 mRNA was confirmed by RT-PCR using total RNA extracted from the glomeruli. Immunohistochemistry using an antibody raised against recombinant rat AQP6 protein could localize the immunoreactivity in a population of collecting duct cells. Serial section observations indicated that the AQP6-immunoreactive cells corresponded to H+ ATPase bearing intercalated cells.