Methods for the analysis of urinary GAGs that can be used for or are applicable to routine assays are described. The most popular method for isolation of GAGs from a urine sample is CPC precipitation, in spite of the fact that it is time-consuming. To identify the different types of GAGs excreted, separation by one-dimensional cellulose acetate electrophoresis followed by staining with alcian blue or toluidine blue may suffice for routine purposes. Solvents such as barium acetate, calcium acetate, barbital buffer and pyridine-formic acid are used for the separation. However, the separation of the seven types of GAGs by conventional one-dimensional electrophoresis is difficult, and a discontinuous electrophoretic method with barium acetate buffer and barium acetate buffer containing ethanol has proved effective for the separation. HPLC separation methods are used for assaying the profiles of enzymatic digestion products of GAGs. Advanced HPLC methods for separating intact GAGs of different types are currently unavailable. Unsaturated disaccharides produced with heparitinase and/or heparinase from heparan sulphate and oligosaccharides produced by hyaluronidase digestion of hyaluronic acid can be separated by HPLC. For chondroitin sulphate isomers, unsaturated disaccharides produced by digestion of the samples with chondroitinase ABC or chondroitinase AC are separated by HPLC and determined by their UV absorbance or by fluorescence labelling. Highly sensitive quantitation of chondroitin sulphate isomers is possible by these methods, which are also efficient for the investigation of the constituents of GAG polymers. Some of these methods have been applied to urine samples from patients with, e.g., mucopolysaccharidoses.