A fluorescence assay was developed to measure the rate of fusion of highly purified clathrin-coated vesicles isolated from bovine brain with purified lysosomes isolated from bovine kidney. Coated vesicles and stripped vesicles, prepared by removal of clathrin from coated vesicles with dilute alkaline buffer, were labeled with the nonfluorescent dye 6-carboxydiacetylfluorescein. Fusion of the vesicles with lysosomes resulted in mixing of the vesicle contents and exposure of 6-carboxydiacetylfluorescein to lysosomal esterases, which hydrolyze the probe's acetate groups to give the fluorescent 6-carboxyfluorescein. Fusion was therefore measured by recording the increase in fluorescence obtained upon mixing the vesicles with lysosomes. The results of the experiments indicated that the clathrin coat of coated vesicles inhibited the fusion of the vesicle membrane with that of the lysosome. In addition, fusion appears to require free Ca2+ and does not require vesicle-surface protein.