Oesophageal atresia with or without tracheo-oesophageal fistula, ileal atresia and Hirschsprung’s disease are surgical malformations of the gastrointestinal tract typically diagnosed early in the neonatal period and varying in severity and prognosis. This report describes a full-term male newborn presenting simultaneous oesophageal atresia with distal tracheo-oesophageal fistula, ileal atresia and Hirschsprung’s disease. In addition to the complex types of gastrointestinal malformations involved, the combination of ileal atresia and Hirschsprung’s disease, as well as ganglion cells distal to intestinal atresia, resulted in a challenging diagnosis. Despite a successful outcome, the patient presented increased morbidity and prolonged hospitalisation. We highlight some important findings that may aid the early diagnosis of Hirschsprung’s disease in this clinical setting. To our knowledge, the association of oesophageal atresia/tracheo-oesophageal fistula, ileal atresia and Hirschsprung’s disease has not been previously reported.