Tracheo-oesophageal fistula (TOF) and oesophageal atresia (OA) represent a series of anatomical abnormalities presenting for emergency surgery in the neonatal period. They present the anaesthetist with cardio-respiratory challenges in the preoperative, intra-operative and postoperative phases. In addition to the consequences of the pathology itself, co-morbidities are very common, which superimpose further considerations. The basic science, anatomy and genetics are discussed as well as the clinical presentation, perioperative management, controversies and complications. The evidence for optimum management is based mostly on expert opinion; there are very few large randomised controlled trials concerning many areas of perioperative management.