Membrane structures of the mixtures of ganglioside G_M1 and endosome specific lipid, bis (monoacylglycero) phosphate (BMP, also known as lysobisphosphatidic acid) were examined at various pH conditions by freeze-fracture electron microscopy and small-angle x-ray scattering. At pH 8.5–6.5, a G_M1/BMP (1:1 mol/mol) mixture formed small vesicular aggregates, whereas the mixture formed closely packed lamellar structures under acidic conditions (pH 5.5, 4.6) with the lamellar repeat distance of 8.06nm. Since BMP alone exhibits a diffuse lamellar structure at a broad range of pH values and G_M1 forms a micelle, the results indicate that both G_M1 and BMP are required to produce closely stacked multilamellar vesicles. These vesicles resemble membranous cytoplasmic bodies in cells derived from patients suffering from G_M1 gangliosidosis. Similar to G_M1 gangliosidosis, cholesterol was trapped in BMP vesicles in G_M1- and in a low pH-dependent manner. Studies employing different gangliosides and a G_M1 analog suggest the importance of sugar chains and a sialic acid of G_M1 in the pH-dependent structural change of G_M1/BMP membranes.