Non-typeable (acapsular) Haemophilus influenzae (NTHi) is a major cause of otitis media accounting for 25–30% of all cases of the disease. Lipopolysaccharide (LPS) is an essential and exposed component of the H. influenzae cell wall. A characteristic feature of H. influenzae LPS is the extensive inter-strain and intra-strain heterogeneity of glycoform structure which is key to the role of the molecule in both commensal and disease-causing behavior of the bacterium. However, to characterize LPS structure unambiguously is a major challenge due to the extreme heterogeneity of glycoforms that certain strains express. A powerful tool for obtaining sequence and branching information is multiple-stage tandem ESI-MS (ESI-MS n ) performed on dephosphorylated and permethylated oligosaccharide material using an ESI-quadrupole ion trap mass spectrometer. In general, permethylation increases the MS response by several orders of magnitude and sequence information is readily obtained since methyl tagging allows the distinction between fragment ions generated by cleavage of a single glycosidic bond and inner fragments resulting from the rupture of two glycosidic linkages. Using this approach we are now able to identify all isomeric glycoforms in very heterogeneous LPS preparations.