Disaccharides tagged with p-aminobenzoic acid (ABA) were separated by capillary electrophoresis (CE) and analyzed on-line with negative ion electrospray ionization tandem mass spectrometry (ESI/MS/MS). The formation of glycosylamine instead of reductive amination was selected as the derivatization reaction. In negative ion ESI, the glycosylamine approach provides more information on linkage and anomeric configuration than reductive amination. In CE analysis of ABA-labeled disaccharides, alpha-cyclodextrin (CD) was found to play a crucial role in the separation of linkage isomers. Although ammonium acetate/alpha-CD provided the best resolution of linkage isomers, the borate buffer was superior to alpha-CD in the separation of disaccharides with the same linkage but different anomeric configuration and/or monosaccharide composition. Both alpha-CD and borate suppressed the ion signal in ESI, and operational conditions were successfully obtained using 10 mM alpha-CD or 10 mM borate.