Hunter syndrome is characterized by a deficiency of iduronate 2-sulfatase. A large number of mutations in the gene have been reported. We describe here the development of a limited primer method for the identification of mutations. In the reaction mixture designed for the limited primer extension, one or two deoxynucleotides from the four necessary deoxynucleotides are added as "selected nucleotides" and another deoxynucleotide which is radiolabeled is added as the "limited nucleotide". The absence of one or two of the deoxynucleotides limits the length of primer elongation, and the low concentration of the "limited nucleotide" causes an "extension-delay" effect and results in a banding pattern upon electrophoresis of the products thus making it possible to distinguish mutant and normal alleles. We have studied three novel mutations in exon IX, 407delTT (TTT to T), 423insCC (CCC to CCCCC), and W502X (TGG to TAG) of the iduronate 2-sulfatase gene by the limited primer extension method.