To date, three genes have been identified as susceptibility genes for Hirschsprung's disease (HSCR), the RET proto-oncogene, the endothelin-B receptor gene (EDNRB) and the endothelin-3 gene (EDN3). However, the question of whether these genes play a role in sporadically occurring HSCR has not been fully clarified. In this study, the authors performed mutation analysis of these three genes in 41 sporadic HSCR patients without any family history by using single-strand conformational polymorphism or denaturing gradient gel electrophoresis methods. Exon 2, 3, 5, 6, 12, 13, 15, and 17 of the RET gene, 7 exons of the EDNRB gene, and the region of the EDN3 gene including sequences corresponding to proteolytic cleavage sites and mature endothelin-3 were analysed. By direct sequencing, three causative RET mutations were confirmed; a Phe to Ser substitution at codon 174, a Cys to Tyr substitution at codon 197, and a point mutation at the splice acceptor site of intron 12, in patients with aganglionosis confined to the rectosigmoid colon, the transverse colon, and the total colon, respectively. In the EDNRB locus, two mutations were observed; a nonsense mutation of Trp to stop at codon 275, and a T insertion at nucleotide 878, in patients with aganglionosis confined to the rectosigmoid colon, and the descending colon, respectively. No mutation was detected in the EDN3 gene. Mutation rates were 7.3% in the RET and 5% in the EDNRB gene. Our data indicate that RET and EDNRB mutations have a role in the aetiology of some sporadically occurring HSCR. However, the low mutation rate of susceptibility genes in sporadically occurring HSCR suggests that other genes or environmental factors are involved in the development of the disease.