We report here that the system y⁺ cationic amino acid transporter ATRC1 localized to clusters within the basolateral membrane of polarized Madin-Darby canine kidney and human embryonic kidney (HEK) cells, suggesting that the transporters are restricted to discrete membrane microdomains in epithelial cells. Based on solubility in nonionic detergents, two populations of ATRC1 molecules existed: approximately half of the total ATRC1 in HEK cells associated with the actin membrane cytoskeleton, whereas another one-fourth resided in detergent-resistant membranes (DRM). In agreement with these findings, cytochalasin D reduced the amount of ATRC1 associated with the actin membrane cytoskeleton. Although some ATRC1 clusters in HEK cells colocalized with caveolin, the majority of ATRC1 did not colocalize with this marker protein for a type of DRM called caveolae. This distribution of ATRC1 is somewhat different from that reported for pulmonary artery endothelial cells in which transporters cluster predominantly in caveolae, suggesting that differences in the proportion of ATRC1 in specific membrane microdomains correlate with differences in the physiological role of the transporter in polarized kidney epithelial vs. vascular endothelial cells.