The present investigation describes the use of on-line chromatographic preconcentration coupled to capillary zone electrophoresis-electrospray mass spectrometry (cPC-CZE-ES-MS) for trace level analysis of negatively charged lipopolysaccharides (LPS) obtained from pathogenic strains of Haemophilus influenzae. The analytical performance of two different types of adsorption media [i.e., C18 irregular particles and poly(styrene-divinylbenzene) membrane] for anionic analytes was first evaluated using a mixture of peptide standards to determine the overall sensitivity of this approach. These chromatographic preconcentrators provided an enhancement of sample loadings of up to 5 microliters with good linear response and low nM concentration detection limits for most peptides investigated. The application of cPC-CZE-ES-MS is further demonstrated for extracts of O-deacylated LPS obtained from H. influenzae strain Eagan. In combination with novel enzymatic releasing methods using proteinase K, this technique provides unparalleled sensitivity and enabled the identification of LPS surface antigens from as little as five bacterial colonies.