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Objective To investigate the mutation of endothelin receptor B (EDNRB) gene and endothelin-3 (EDN-3) gene in sporadic Hirschsprungs disease (HD) in Chinese population. Methods Genomic DNA was extracted from bowel tissues of 34 unrelated HD patients which were removed by surgery. Exon 3, 4, 6 of EDNRB gene and Exon 1, 2 of EDN-3 gene were amplified by polymerase chain reaction (PCR) and analyzed by single strand conformation polymorphism (SSCP).Results EDNRB mutations were detected in 2 of the 13 short-segment HDs. One mutant was in the exon 3; the other one was in the exon 6. EDN-3 mutation was detected in 1 of the 13 short-segment HDs and in the exon 2. Both EDNRB mutation and EDN-3 mutation were detected in one short-segment HD. No mutations were detected in the ordinary or long-segment HD. Conclusion The mutations of EDNRB gene and EDN-3 gene are found in the short-segment HD of sporadic Hirschsprungs disease in Chinese population, which suggests that the EDNRB gene and EDN-3 gene play important roles in the pathogenesis of HD. the mutations of EDNRB and EDN-3 lead to the maldevelopment of the enteric nervous system.