The Mucopolysaccharidoses (MPS) are lysosomal storage disorders that result from defects in the catabolism of glycosaminoglycans. Impaired muscle, bone and connective tissue are typical clinical features of MPS due to disruption of the extracellular matrix. Markers of MPS disease pathology are needed to determine disease severity and monitor effects of existing and emerging new treatments on disease mechanisms. Urine samples from a small cohort of MPS-I, II and VI patients (n=12) were analysed using label-free quantative proteomics. Fifty three proteins including many associated with extracellular matrix organisation were differently expressed, A targeted multiplexed peptide MRM LC-MS/MS assay was used on a larger validation cohort of patient samples (MPS-I n= 10, MPS-II n= 15, MPS-VI n= 5, Control n=20). MPS-I and-II groups were further sub-divided according to disease severity. None of the markers assessed were altered significantly in the mild disease groups compared to controls. Beta-galactosidase, a lysosomal protein, was elevated 3.6-5.7-fold significantly (p<0.05) in all disease groups apart from mild MPS-I and II. Collagen type I alpha, fatty-acid-binding-protein 5, nidogen-1, cartilage oligomeric matrix protein and insulin-like growth factor binding protein 7 concentrations were elevated in severe MPS I and II groups. Cartilage oligomeric matrix protein, insulin-like growth factor binding protein 7 and beta-galactosidase were able to distinguish the severe neurological form of MPS-II from the milder non-neurological form. Protein Heg1 was significantly raised only in MPS-VI. This work describes the discovery of new biomarkers of MPS that represent disease pathology and allows the stratification of MPS-II patients according to disease severity.