Four 6-O-substituted saccharides, namely 6-O-vanillyl-d-glucose 1, 6-O-vanillyl-d-mannose 2, 6-O-iso-vanillyl-d-glucose 3 and 6-O-iso-vanillyl-d-mannose 4 have been synthesized. Synthesized saccharide derivatives have been subsequently used in Mo(VI)-catalyzed stereospecific isomerizations yielding compounds with potential radical scavenging activity. In order to accelerate intramolecular isomerization rates and conversions microwave irradiation was used. Synthesized products were obtained with excellent stereoselectivity in good conversions and were tested by EPR spectroscopy for radical scavenging activity.