In recent years, the palliative treatment of Hypoplastic Left Heart Syndrome (HLHS) with a three-staged surgical repair has gained widespread acceptance in North America and elsewhere and has significantly improved the life-expectancy of these children. We report on a child in whom the diagnosis of cystic fibrosis (CF) was made shortly after the first-stage palliation (modified Norwood procedure), and in which surgical palliation was successfully completed with second- (bidirectional Glenn) and third-stage (fenestrated Fontan) procedures. During this period, the child suffered several CF-related complications, i.e. repeated respiratory failure, meconium ileus and coagulation abnormalities, which required adjustment of the anaesthesia, surgical and intensive care management. Considering the trend to perform surgical corrections of major cardiac defects in the early neonatal period, before concomitant genetic diseases are discovered, paediatric cardiac anaesthesiologists, surgeons and intensivists may be confronted with more cases of open heart surgery in infants with CF in the future.