The present invention provides biomarkers for efficient and accurate characterization of Sanfilippo syndrome. In particular, the present invention provides biomarkers differentially expressed in Sanfilippo syndrome. Those biomarkers, used alone or in combination, may permit more accurate robust characterization of Sanfilippo syndrome, resulting in more precise determination of the types and/or severity of the syndrome. In addition, inventive biomarkers according to the present invention can be used to effective monitor treatment response in Sanfilippo syndrome patients and/or to optimize treatment for Sanfilippo syndrome.