Recombinant activated factor V11 (rFV11a) is a relatively new procoagulant agent and its place in surgical practice continues to be investigated. We report the use of rFV11a to help manage bleeding in the operating theatre in a neonate, following weaning from cardiopulmonary bypass for arterial switch procedure, when bleeding continued in spite of maximal medical therapy and apparent exclusion of a surgical cause of bleeding. In this patient administration of rFV11a failed to facilitate haemostasis and cardiopulmonary bypass was re-instituted allowing location and repair of a small awkward surgical source. Separation from this additional 20 min of bypass was successful but a large thrombus was noted in the membrane oxygenator of the extracorporeal circuit in spite of the presence of adequate ‘laboratory’ markers of anticoagulation in the pump blood. No adverse sequelae to the patient occurred.