A proton pump, the vacuolar ATPase, is known to generate the acidic lumenal environment of endosomes and lysosomes. We have investigated the role of the vacuolar ATPase in endocytic membrane traffic by combining electron microscopy in vivo with a cell-free assay that reconstitutes endosome fusion in vitro. Our observations show that inactivation of this proton pump with bafilomycin A1 has no significant effects on internalization or recycling back to the plasma membrane. However, early endosomes become highly tubular and endocytosed markers do not appear in late endosomes. Our data strongly suggest that, upon inactivation of the proton pump, the formation of a vesicular intermediate between early and late endosomes, which we term endosomal carrier vesicle, is impaired.