The oxidation of per‐O‐acetyl S‐(1→3)‐ and S‐(1→4)‐linked thiodisaccharides containing glucose, gulose and galactose residues with an excess of m‐chloroperbenzoic acid gave the corresponding sulfoxides or sulfones. Sulfones were formed when the oxidation reaction was left for longer times. The sulfoxides were obtained as diastereomeric mixtures due to the chirality of the sulfur atom. Both diastereoisomers of the S‐(1→3)‐linked thiodisaccharide sulfoxides were isolated by column chromatography, whereas the S‐(1→4)‐linked analogues could not be separated. The absolute configuration of the sulfur stereocentre of the sulfoxides was assigned using NMR spectroscopy, taking into account the preferred conformations of the molecules, and the shielding/deshielding of proton signals caused by the anisotropy of the S=O bond and related effects. Most of the thiodisaccharide sulfoxides were successfully O‐deacetylated with MeOH/Et3N/H2O, but the sulfones underwent elimination reactions under these conditions. Therefore, the oxidation was performed on unprotected thiodisaccharides, and the corresponding sulfones were obtained in very good yields.