Anaesthetic care during thoracic surgical procedures in neonates combines components of the knowledge bases of neonatal anaesthesia with those of thoracic anaesthesia. This chapter reviews the principles of anaesthesia during thoracic surgery in neonates including the pre-operative evaluation, anaesthetic induction techniques, maintenance anaesthesia and options for post-operative analgesia. In addition, given the need to provide optimal surgical visualisation during these procedures, one-lung ventilation (OLV) may be required. Techniques to provide OLV in the neonate and the principles of anaesthetic care during OLV are reviewed. Finally, specific scenarios of neonatal thoracic surgery are reviewed including anaesthetic care during: (1) laryngoscopy and rigid bronchoscopy, (2) thoracoscopy, (3) repair of tracheo-oesophageal fistula, (4) resection of congenital cystic adenomatoid malformation, and (5) treatment of congenital lobar emphysema.