BACKGROUND: Esophageal atresia (EA) is one of the most common congenital digestive anomalies. With improvements in surgical techniques and intensive care treatments, the focus of care of these patients has shifted from mortality to morbidity and quality-of-life issues. These children face gastrointestinal (GI) problems not only in early childhood but also through adolescence and adulthood. There is, however, currently a lack of a systematic approach to the care of these patients. The GI working group of International Network on Esophageal Atresia comprises members from ESPGHAN/NASPGHAN and was charged with the task of developing uniform evidence-based guidelines for the management of GI complications in children with EA. METHODS: Thirty-six clinical questions addressing the diagnosis, treatment, and prognosis of the common GI complications in patients with EA were formulated. Questions on the diagnosis, and treatment of gastroesophageal reflux, management of "cyanotic spells," etiology, investigation and management of dysphagia, feeding difficulties, anastomotic strictures, congenital esophageal stenosis in EA patients were addressed. The importance of excluding eosinophilic esophagitis and associated GI anomalies in symptomatic patients with EA is discussed as is the quality of life of these patients and the importance of a systematic transition of care to adulthood. A systematic literature search was performed from inception to March 2014 using Embase, MEDLINE, the Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Clinical Trials, and PsychInfo databases. The approach of the Grading of Recommendations Assessment, Development and Evaluation was applied to evaluate outcomes. During 2 consensus meetings, all recommendations were discussed and finalized. The group members voted on each recommendation, using the nominal voting technique. Expert opinion was used where no randomized controlled trials were available to support the recommendation.