A procedure for determining the amino acid and sugar composition of streptococcal peptidoglycan-polysaccharide complexes by capillary gas chromatography-mass spectrometry (GC-MS) was established. Amino acids are analysed as butyl heptafluorobutyl derivatives and sugars as alditol acetates. These two different groups of compounds are derivatized independently but chromatography in both cases utilizes the same OV-1701 fused-silica capillary column which simplifies GC-MS analysis. The butyl heptafluorobutyl procedure incorporates new pre- and post-derivatization clean-up steps. Additionally, selected-ion monitoring MS allows amino acids to be readily analysed without interference from background noise.