A short-segment Hirschsprung disease (HSCR) patient associated with 21 trisomy showing point nucleotidic changes in both the receptor tyrosine kinase (RET) proto-oncogene and the endothelin-B receptor (EDNRB) gene is reported. A T to A heterozygous transition at the splicing donor site of the intron 10 in the RET proto-oncogene, and a G to A heterozygous substitution in non-coding region in the exon 1 of the EDNRB gene were observed. The familial analysis with these genes revealed that the origin of the former mutation was de novo and the latter one was maternal. No patient has been reported with two points mutations in different pathogenetically susceptible loci for HSCR. There is genetic evidence that the RET and EDNRB genes may interact in their susceptibility leading to HSCR.