Uncertainty exists regarding the degree to which infants with congenitally malformed hearts are at risk of behavioural disorders in childhood. Data was collected as part of a randomized clinical trial involving 155 children with surgically corrected transposition (concordant atrioventricular and ventriculo-arterial connections or alignments). As infants, they underwent the arterial switch operation, involving deep hypothermia with predominantly total circulatory arrest or predominantly low-flow continuous cardiopulmonary bypass as the method of providing support to the vital organs. Parents completed the Child Behavior Checklist when the patients were aged 4 and 8 years, and the Connors' Parent Rating Scale at the age of 8 years. When the children were aged 8, teachers completed the Teacher's Report Form and the Connors' Teacher Rating Scale. In the cohort as a whole, the frequencies of behavioural problems identified by both parents and teachers were elevated, particularly on the scales for competence of the Child Behavior Checklist, and the Adaptive scales of the Teacher's Report Form. Approximately 1 in 5 patients had scores for Total Problem Behavior in the range of clinical concern on both the Child Behavior Checklist and the Teacher's Report Form. Few differences were found, however, according to the method of operative treatment. Postoperative seizures were associated with social and attention problems. Children experiencing academic problems at the age of 8 showed a larger increase in behavioural problems between the ages of 4 and 8 than did children making adequate academic progress. Children with congenitally malformed hearts who underwent reparative surgery in infancy using a strategy of severe haemodilution and alpha stat are at increased risk of behavioural problems in middle childhood.