Rapid and reliable methods for the analysis of O- and C-allyl galactopyranosides and glucopyranosides are presented, based on capillary zone electrophoresis (CZE) and micellar electrokinetic capillary chromatography (MEKC). In MEKC, the formation of chromophoric and charged complexes between the saccharides and borate as well as the hydrophobic interactions with micelles jointly contributed to the selective separation and sensitive detection of all the investigated anomeric couples. Some non-purified synthesis mixtures of C-allyl glycosides were successfully characterised without pre-treatment. MEKC buffer conditions for which glycosides separation was successfully achieved were then exported and applied to reverse-phase liquid chromatography (RP-HPLC), for the quantitative isolation of each allyl glycoside anomer. Identification of the obtained anomeric products was performed by electrospray mass spectrometry and (13)C NMR spectroscopy. Glycoside-solvent interactions driving the selective anomeric separation were shortly addressed and discussed on the basis of sugar derivatives structural differences.