Addition of a sugar residue to a pyridylamino (PA) sugar chain affects its elution time on reverse-phase HPLC and the contribution of the sugar residue is not influenced by the other sugar residues [S. Hase, S. Natsuka, H. Oku, and T. Ikenaka (1987) Anal. Biochem. 167, 321-326]. The partial relative elution times (Ei) of 22 sugar residues were calculated from the relative elution times (the elution time relative to Man5Glc-NAc2-PA) of three kinds of PA-sugar chain: the oligomannose and N-acetyllactosamine types and sugar chains with a xylose residue. The relative elution time of a PA-sugar chain can be calculated by summing the Ei values of all of the constituent sugar residues. The calculated relative elution times of 44 PA-sugar chains agreed well with the observed values. This method can be used to estimate the relative elution times of PA-sugar chains that are not yet available, and to estimate the structures of sugar chains in limited amounts of glycoproteins by a combination of sugar composition analysis and exoglycosidase digestion.