N-Glycosidically linked oligosaccharides were released from glycoproteins by digestion with trypsin followed by hydrazinolysis and subsequently re-N-acetylated and reductively pyridylaminated. Derivatives of sialic acid-containing oligosaccharides were further desialylated with neuraminidase. The final derivatives of asialo-oligosaccharides were analyzed by capillary zone electrophoresis in two carriers, an acidic phosphate buffer and an alkaline borate buffer. The former carrier allowed direct zone electrophoresis as cationic immonium ions, accordingly size-dependent separation, whereas the latter realized indirect electrophoresis as anionic borate complexes, i.e., separation based on the structural variation in outermost monosaccharide residues. Two-dimensional plots of relative mobilities of the derivatives in these dual separation modes to reductively pyridylaminated glucose provided a good tool for identification of oligosaccharides.