We report the anaesthetic management of a male neonate with congenital cyst adenoid malformation (CCAM) of the lung who underwent thoracotomy for resection of CCAM 24 h after birth and again at 24 days. The initial operation involved a 10-day admission to a paediatric intensive care unit (PICU) requiring ventilation, and was complicated by a pneumothorax. This report concentrates on the anaesthetic management for the second thoracotomy. The combination of intra-operative remifentanil infusion and the use of ultrasound to confirm correct placement of epidural catheter allowed on-table tracheal extubation and a shorter stay in PICU. The use of one-lung ventilation (OLV) allowed for better surgical access and enabled complete resection of the lesion.