AbstractChondroitin sulfate (CS) is a widely studied class of glycosaminoglycans, responsible for diverse biological functions. Structural analysis of CS is generally based on disaccharide analysis. Sample preparation is a key analytical issue in this case. However, a detailed study on the stability and recovery of CS-derived species has been lacking so far. We have found that for solvent exchange, in general, vacuum evaporation (SpeedVac) is much preferable than lyophilization. Moreover, in the case of aqueous solutions, higher recovery was experienced than in solutions with high organic solvent content. Storage of the resulting disaccharide mixture in typical HPLC injection solvents is also critical; decomposition starts after 12 h at 4 °C; therefore, the mixtures should not be kept in the sample tray of an automatic injector for a long time. The study, therefore, lays down suggestions on proper sample preparation and measurement conditions for biologically derived chondroitin sulfate species.