The membrane of each organelle has its own characteristic/specific lipid composition. The integrity of the lipid composition is essential for the organelles to maintain their surface properties, structure and functions. Late endosomes are the organelles which have roles in the intracellular macromolecule sorting as well as the degradation and metabolism of materials in the cell, and are rich in the negatively-charged unusual phospholipid, bis (monoacylglycero) phosphate (BMP). The structure of the late endosome is altered from multivesicular to multilamellar membranes under different pathological conditions, such as glycolipid-storage diseases, and by treatment with certain drugs, resulting in a disruption of the exit of cholesterol from the organelle. The molecular mechanisms of these phenomena have not been revealed. In this report, we show that the structural change of these organelles can be reproduced in vitro by incubating BMP membrane with glycolipids as well as a certain drug. It is also shown that cholesterol is trapped in such an in vitro system.