Oesophageal atresia is a congenital developmental defect of alimentary tract concerning the interruption of oesophagus with or without connection with the trachea. The incidence of oesophageal atresia is 1:3000-3500 of live-born infants. Associated anomalies occur in 50% of patients (syndromic cases). In the rest of the patients with oesophageal atresia these anomalies are isolated (non-syndromic cases). The knowledge of dysmorphic syndromes with oesophageal defects, allows us to diagnose the complex genetic syndromes and to implement the correct treatment and correct genetic counselling concerning the etiology, natural course of the disease, prognosis and possible complications as well as determining the recurrence risk of the disease in the family. The authors describe the chosen embryological, epidemiological and genetic aspects of congenital oesophageal atresia. The clinical aspects, genetic counselling as well as the genetic basis of chosen genetic syndromes with oesophageal atresia are also described in this article.