Background: Vacuolar H+-ATPases (V-ATPases) are essential for renal bicarbonate transport in both the proximal and distal nephron. Regulation of proton transport occurs, in part, by vesicle-mediated traffic of V-ATPases between intracellular vacuoles and the plasma membrane. Although the proteins involved in regulated V-ATPase traffic are largely unknown, Rab GTPases have a central role in the traffic and recycling of other membrane proteins. Methods: To identify candidate Rab GTPases potentially involved in V-ATPase traffic, immunocytochemical and subcellular fractionation studies were used to evaluate the distribution to sites of abundant V-ATPase of 5 Rab GTPases expressed in kidney, Rab5a, Rab11, Rab13, Rab18, and Rab20. Results: The immunocytochemical distribution of Rab5a and Rab13 and the subcellular distribution of Rab18 were not compatible with a role in V-ATPase traffic. In contrast, Rab11 colocalized with V-ATPase in apical regions of proximal tubule, and Rab20 colocalized with the enzyme in intercalated cells. Rab11 and Rab20 were enriched in membrane fractions that were also enriched in V-ATPase B2 and B1 subunit isoforms, respectively. Conclusions: The immunohistochemical data in combination with the membrane fractionation studies are consistent with a potential role for Rab11 and Rab20 in regulating V-ATPase traffic in specific segments of the nephron. Copyright © 2005 S. Karger AG.