The authors present the results of a morphological study of the biological samples from patients treated with the inferior esophageal atresia with tracheoesophageal fistula, which included immunohistochemical examination of neuronal changes in the esophageal wall, predominantly in the anomalous segment, with the need surgical involvement. The results obtained in the control group shows that the period of 36-37 weeks of gestation there is persisting glial cell component. The attested features are characteristic for the morpho-functional transition period from prematurity to maturity, being a specific neuronal cytology of the norm in the course of maturation of the child. Congenital morphopathological modifications of intramural ganglio-neural structures determined in both esophageal segments in cases of esophageal atresia with inferior tracheoesophageal fistula, concomitant with fibromuscular dysplasia, may be considered as factors with significant impact on esophageal motility regulation in children with esophageal atresia with tracheoesophageal fistula, and explains within certain limits their role in esophageal dismotility found postoperatively in this group of children.