A series of per-O-methylated flavonoid di- and tri-glycosides, linked with 1-2 and/or 1-6 glycosidic bonds between sugar rings that were isolated from different plant materials were analyzed. It was demonstrated that the fragmentation behavior of permethylated flavonoid glycosides is dependent on the glycosidic bond placement between sugars. Y(n) type fragment ions, created after glycosidic bond cleavage with oxygen retention on sugar at the reducing end for permethylated compounds, were observed in the normal and linked-scan mass spectra recorded for alpha(1-2) bonded conjugates of flavonoid di- and tri-glycosides. Moreover, for alpha (1-6) linked glycosides, Y fragments created after rearrangement and elimination of internal sugar residues were observed in addition to Y(n) type ions, but these fragment ions were not registered in normal desorption ionization spectra. This second type of fragmentation was also reported previously in collision-induced dissociation tandem mass spectrometry (CID MS/MS) spectra of some oligosaccharides and flavonoid glycosides, but their presence was independent of the glycosidic bonds placement between sugar rings.