We have developed a method for the direct analysis of a hypoxanthine-guanine phosphoribosyltransferase (HPRT) allele associated with a deficiency of enzyme activity and an early onset of gout. The functionally abnormal enzyme coded for by this mutant allele (HPRTToronto) differs from the normal enzyme by an arginine-to-glycine substitution at position 50. A single base change in the codon for arginine 50 can explain this substitution. Direct analysis of this point mutation is based on the observation that it abolishes a Taq I recognition site in HPRT DNA. As predicted, DNA from individuals with the HPRTToronto allele exhibited an abnormal restriction pattern when digested with Taq I and probed with HPRT complimentary DNA: a normal 2.0-kb fragment is replaced by a 4.0-kb fragment. The 4.0/2.0-kb restriction fragment variation was used to detect the HPRTToronto allele in a heterozygote that was otherwise normal with respect to the classical techniques used to diagnose heterozygosity in HPRT deficiency.