Capillary electrophoresis enables fast, high efficiency separations of oligosaccharides, wherein positional and/or linkage isomers, bearing the same charge-to-mass ratio, can readily be separated based on hydrodynamic radius differences. Fundamental electrophoretic mobility theory was used to investigate the correlation between changes in hydrodynamic volume equivalent radius and corresponding electrophoretic characteristics of oligosaccharides with different molecular properties. Fluorescently derivatized isomeric malto-, cello-, and isomaltooligosaccharide ladders, differing only in their linkage type of a1?4, beta 1?4, and a1?6, respectively, as well as a sterically larger N-acetylchitooligosaccharide ladder were used as model compounds. Mere differences in glycosidic linkage type or anomericity of isomeric oligo-glucoses had a decisive impact on their electromigration behavior, thus reflecting discrepancies in hydrodynamic radii and associated molecular conformations. The impact of hydrogen bridges, and associated availability of hydroxyl groups, on the molecular conformations, was investigated by hydrophilic interaction liquid chromatography. The experimentally observed electrophoretic and chromatographic differences between isomeric oligo-glucoses strongly suggested that special attention must be given when homooligosaccharide ladders are employed for normalization and comparability purposes, for example, in glucose unit calculation based structural elucidation.