A novel microchip electrophoresis method was developed and applied for sensitive detection and quantitative analysis of endotoxins extracted from Gram-negative bacteria. The method provides a fast and quantitative differentiation of smooth and rough endotoxins based on the solubilization and complexation of the lipopolysaccharides with dodecylsulfate, and then with a fluorescent dye. The migration of the complexes was followed by LIF detection. The novel method is able to replace the SDS-PAGE with the advantage of high speed and better sensitivity, and by avoiding the laborious gel-preparation and silver staining.