Lesch-Nyhan syndrome (LNS) is caused by a severe deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT) and clinically characterized by self-injurious behavior and nephrolithiasis; the latter is treatable with allopurinol, an inhibitor of xanthine oxidase which converts xanthine and hypoxanthine into uric acid. In the HPRT gene, more than 200 different mutations are known, and de novo mutation occurs at a high rate. Thus, there is a great need to develop a highly specific method to detect patients with HPRT dysfunction by quantifying the metabolites related to this enzyme. A simplified urease pretreatment of urine, gas chromatography-mass spectrometry, and stable isotope dilution method, developed for cutting-edge metabonomics, was further applied to quantify hypoxanthine, xanthine, urate, guanine and adenine in 100 microl or less urine or eluate from filter-paper-urine strips by additional use of stable isotope labeled guanine and adenine as the internal standards. In this procedure, the recoveries were above 93% and linearities (r(2)=0.9947-1.000) and CV values (below 7%) of the indicators were satisfactory. In four patients with proven LNS, hypoxanthine was elevated to 8.4-9.0 SD above the normal mean, xanthine to 4-6 SD above the normal mean, guanine to 1.9-3.7 SD, and adenine was decreased. Because of the allopurinol treatment for all the four patients, their level of urate was not elevated, orotate increased, and uracil was unchanged as compared with the control value. It was concluded that even in the presence of treatment with allopurinol, patients with LNS can be chemically diagnosed by this procedure. Abnormality in the levels of hypoxanthine and xanthine was quite prominent and n, the number of standard deviations above the normal mean, combined for the two, was above 12.9.