A sodium-independent neutral and basic amino acid transporter (NBAT) from rat kidney was recently cloned and its amino acid sequence deduced. We used light and electron microscopic immunoperoxidase labeling to determine the cellular localization of NBAT in rat kidney and small intestine. The localization was carried out using site-directed antisera raised against synthetic peptides within NBAT. The most prominent localization of NBAT was in microvilli of epithelial cells lining renal proximal tubules. Microvilli of small intestinal epithelia were less frequently immunoreactive. Unexpectedly, the most intense labeling in the small intestine was seen within enteroendocrine cells and submucosal neurons. The neuronal labeling was highly localized within dense core vesicles in axon terminals apposed to the basal lamina near fenestrated blood vessels. These results support the proposal that NBAT plays a role in reabsorption of amino acids in renal tubules. In addition, they suggest that NBAT (or NBAT-like proteins) may have multiple functions in the small intestine, including luminal uptake of amino acids and vesicular uptake of related substrates into enteroendocrine cells and enteric neurons.