Separation of reduced and permethylated olgisaccharides by gas chromatography can be facilitated by the use of a fused silica capillary column coated with methyl silicon. The presence of N-acetylhexosamines in oligosaccharides increases their rentention time and interferes with efficient GC separation. Transamidation of hexosamines by triflouroacetolysis followed by reduction, removal of O-tri-fluroacetyl groups and permethylation, dramatically reduces the rentention time of hexosamine-containing olgiosaccharides and permits separation of olgiosaccharides containing up to six monosaccharide units, regardless of how many of these are hexosamines. The mass spectra of permethylated olgiosaccharides with N-trifluoro-acetylated amino sugars show unexpectedly high abundances of mass ions containing the N-trifluoroacetyl group. As many of these ions are large, they provide useful information regarding oligosaccharide structure.