Acidic O-glycans having sialic acid and/or sulfate residue are abundantly expressed in intestinal mucins. However, structural elucidation of acidic O-glycans is a laborious and time-consuming task due to their large structural variations. Here, we describe a methodology of structural elucidation for sialylated O-glycan alditols from intestinal mucins using tandem mass spectroscopy. Methylesterification and mild periodate oxidation of sialylated O-glycan alditols assist mass analysis. This description includes the purification process of O-glycan alditols for structural analysis.