The patients treated for oesophageal atresia present a correlation between the clinical sintomatology after recanalization characterized by disfagia, dispnea, recurrent cough, chronic pneumopaties and oesophageal anomalies. Where morphological alterations accounting for the presence of gastro-oesophageal reflux (GOR) were not evident, possible functional alterations of the motility were considered. The incidence of GOR was considerably high and, expression of a congenital alteration of the lower oesophageal sphincter and of oesophageal peristalsis, becomes even more severe due to further stretching of the gastro-esophageal junction. The authors underline that the early demonstration of histological changes, even before recanalization, and the motility disorders of the oesophagus have to be well studied, while the LES is normalized, in order to prevent and treat the possible appearance of the well-known complications of GOR.