There is evidence that components of the endosomal-lysosomal system of most cells have an acidic interior. The weak base, N-(3-[(2,4-dinitrophenyl)amino]propyl)-N-(3-aminopropyl)methylamine dihydrochloride (DAMP) has been shown to accumulate in acidic compartments in cultured cells and in isolated perfused proximal tubules. We infused DAMP intravascularly in vivo and used colloidal gold immunocytochemistry to identify acidic compartments in cells of the rat glomerulus and proximal tubule. Sprague-Dawley rats were infused intra-arterially with DAMP. The kidneys were fixed by intravascular perfusion with 1% glutaraldehyde and embedded in Lowicryl K4M. Sections were exposed to a mouse anti-dinitrophenol (DNP) monoclonal antibody that cross-reacts with DAMP, followed by gold-conjugated goat anti-mouse immunoglobulin G. Transmission electron microscopy revealed positive labeling of the lysosome-like structures of the various cells of the glomerulus and lysosomes, endosomes, and numerous endocytic vesicles of all segments of the proximal tubule. We conclude that 1) DAMP can be used in vivo to identify acidic compartments in the kidney and 2) lysosomes, endosomes, and many endocytic vesicles of the rat proximal tubule as well as lysosome-like structures in cells of the glomerulus have an acidic interior.