Abnormal distribution of the enteric nerves such as adrenergic, cholinergic and peptidergic nerves may cause the functional obstruction in Hirschsprung's disease (HD). Although the sustained contraction of the aganglionic segment is the main pathophysiology of HD, the etiology and pathogenesis is not thoroughly understood. With the recent progress of molecular biology and genetics,a more detailed approach to the pathogenesis of the HD can be undertaken. In this review, the roles of the nitric oxide, nitric oxide synthase and interstitial cells of Cajal on smooth muscle relaxation, the effects of extracellular matrix, cell adhesion molecules, neurotrophic factors on the migration and maturation of the neural crest cells are described. In the section of genetic factors, familial occurrences, association of chromosomal abnormalities, RET gene, glial cell line-derived neurotrophic factor gene, endothelin-3 gene and endothelin-B receptor gene and their relationships to HD is briefly reviewed.