We report the first case of hypertrophic pyloric stenosis in an intrathoracic stomach in a neonate with congenital ultra-short oesophagus and iniencephaly clausus. Antenatal ultrasound detected right-sided thoracic cystic lesions and postnatal investigations revealed an intra-thoracic stomach and spleen with an ultra-short oesophagus and intact diaphragm. Subsequently, she developed pyloric stenosis. Such neonates require urgent referral to surgical centres for what is a challenging diagnosis and complicated management.