Esophageal atresia is a rare condition (1:2,500-4,500), incompatible with life, and a surgical emergency in the neonatal period. It is associated with prematurity in 30% of cases, and to congenital abnormalities in 50% of cases, especially cardiac anomalies. Major congenital heart diseases and low weight are independent predictors of mortality and critical perioperative events. The aim of this article is to describe the most significant anaesthetic challenges presented in a case of a term neonate undergoing emergency surgery after being diagnosed with esophageal atresia, tracheoesophageal fistula type iiib/C, and imperforate anus. The major priorities during the anaesthetic management consist of establishing a safe airway and effective pulmonary ventilation that minimises air leakage to the upper digestive tract.