Iatrogenic oesophageal perforation in neonates is well recognized in the medical and surgical literature with intubation injury listed as a possible contributing mechanism besides nasogastric tube placement and suctioning. Diagnosis can be difficult and sometimes confused with other entities. With early diagnosis, nonsurgical management often leads to complete resolution in neonates. We report the case of a 1-day-old premature neonate who was brought to the operating room with the preliminary diagnosis of proximal oesophageal atresia with stump perforation and distal tracheo-esophageal fistula. His intubation for respiratory distress at birth had been difficult due to Pierre-Robin sequence with micrognathia. Oesophagoscopy in the operating room revealed a patent oesophagus but perforations in the pharynx and in the proximal oesophagus with the nasogastric tube entering the pharyngeal perforation. Oesophageal perforation and the limitations of the difficult airway algorithm in small neonates are discussed.