Lipopolysaccharide (LPS) is the main component of the outer leaflet of the outer membrane of Gram-negative bacteria. Native isolates of LPS comprise a high inherent heterogeneity. This paper presents the first application of CE to separate and online mass analyze the different constituents of underivatized R-form LPS and lipid A with an FT ion cyclotron resonance mass spectrometer. A Beckman P/ACE MDQ and a home-made CE instrument were coupled to the mass spectrometer using a sheath liquid interface. An optimized CE electrolyte based on water, isopropyl alcohol, triethylamine and acetic acid at pH 8.9 allowed the separation of molecular species even of complex mixtures to a large extent with observed detection limits of single constituents of the samples in the low femtomol range. Comparison of CE-MS and MS measurements under equal conditions enabled the investigation of ion suppression effects in LPS samples.