We report a method of coupled CE-LIF detection with flow cytometry for high-throughput determination and quantitation of fluorophores in single intact K562/S (KS) cells. The membrane properties of KS cell including fluophore transport rate and apparent permeability coefficient were further quantitatively characterized. The method has advantages for accurate quantitation and unique capacity of high-throughput analysis. The strategy will be useful for the quantitation of fluorophores in the intact cells, such as measurement of multidrug resistance, quantitation of specific protein expression, and quantitative characterization of protein and enzyme functions.