Chondroitin sulphates belong to a group of naturally occurring glycosaminoglycans and play a role in many physiological processes including ageing and the effects of various diseases. Research into chondroitin sulphates has found that the most important analytes are 4-and 6-sulphated disaccharides. We developed an HPLC method for the separation and quantification of underivatized chondroitin/dermatan sulphates—unsaturated disaccharides (4-and 6-sulphated disaccharides). This method is based on the separation of disaccharides by amido as well as amino columns under acidic conditions. These columns enabled the successful separation of 4-and 6-sulphated disaccharides using 50 (amido column) and 25 mmol/L (amino column) phosphate buffer, pH 4.25 (detection at 230 nm), at retention times of less than 10 min. The limit of quantification was 0.5 µg/mL. The applicability of this method was demonstrated through analysis of unsaturated disaccharides produced from the enzymatic digestion of chondroitin/dermatan sulphates of the solubilized extracellular matrix produced from porcine urinary bladder and human umbilical cord.