The vacuolar H(+)-ATPase provides a channel through which protons can be pumped across the bilayer. It is a complex assembly of about 20 subunits made up from 13 different polypeptide chains. The proton channel is located in the bilayer and therefore must be formed from one or both of the two intramembraneous subunits, called in yeast Vphlp (100 kDa) and Vma3p (16 kDa). Electron microscopy and the use of water soluble and hydrophobic chemical probes in conjunction with mutagenesis to cysteine or glutamic acid residues, suggest that the membrane sector consists of a single Vphlp subunit in association with a hexameric complex of the four-helical bundle Vma3p subunit. This hexamer encloses a large central pore lined by the first transmembrane helix. This pore appears to be impermeable, however; instead, a glutamic acid residue critical to transport function is located on the outside of the hexamer, deeply buried in the membrane and accessible to probes and inhibitors resident in the hydrophobic phase of the bilayer. The stoichiometry and chemistry of inhibitor binding supports the postulate that the mechanism of action involves rotation of the hexamer in the plane of the bilayer. Mutagenesis data on the Vphlp subunit indicate that it is vital to proton transport. It is likely, therefore, that the proton channel is formed at the interface of the Vphlp and Vma3p subunits, the protons moving via a network of interacting charged amino acid side-chains.