Neurological involvement in X-linked mucopolysaccharidosis type II (Hunter syndrome) is indicative of more severe disease, but is not attenuated by current enzyme replacement therapy which does not significantly penetrate the blood-brain barrier. Magnetic resonance spectroscopy is an objective method of determining brain metabolites and has the potential to identify disease biomarkers with utility in evaluating current and novel therapies. MRS studies from seven patients with MPSII all receiving enzyme replacement therapy were compared with a large cohort of children with various neurocognitive disorders with normal MR imaging. All studies were completed on 1.5Tesla clinical MR scanners. Brain metabolite concentrations were determined from basal ganglia and parieto-occipital white matter using LCModel quantification. Serial trends in brain metabolites were analysed. Examination of mean spectra and quantitative metabolite concentrations demonstrated significantly decreased white matter N-acetylaspartate (a neuronal marker), total choline and glutamate, and elevated myo-inositol (glial marker) in MPSII patients. Analysis of serial determinations of white matter N-acetylaspartate demonstrated no change in two patients with stable MR imaging features but decreasing N-acetylaspartate in two patients more severely affected or deteriorating. These data demonstrate the utility of MRS to monitor serial alterations in brain metabolites including N-acetylaspartate which could be used as biomarkers of progressive neurological disease in MPSII. Integrated as an adjunct to MRI, such an approach could aid the evaluation of the efficacy of current ERT and also novel CNS-targeted therapies in MPSII.