Surgical correction greatly decreases the mortality and cardiac morbidity of cyanotic congenital heart disease, but children remain at risk of long term difficulties in other areas. A historical cohort study was conducted to determine the relation between heart disease and school performance in 29 children aged 7 to 12 years old with simple transposition of the great arteries or tetralogy of Fallot. All children had surgical correction of their lesion before 2.5 years of age. Those at greater risk of school difficulties because of recognised complications of their heart disease or for reasons other than directly attributable to the heart disease were excluded. Comparison was made with 36 children who had presented with cardiac murmurs at a similar age, but who did not require treatment. Children with cyanotic disease showed significantly poorer performance in all academic areas assessed by the Wide Range Achievement Test-Revised; the difference in group mean score (adjusted for differences in maternal education, sex, and parental occupational prestige) for reading was 10.3 points (confidence interval (CI) 1.25 to 19.34), for spelling 7.8 (CI 1.11 to 14.52), and for arithmetic 6.8 (CI 0.19 to 13.39). The differences in adjusted group means for the Wechsler Intelligence Scale for Children-Revised full scale, performance and verbal IQs were significant, particularly the later at 10.1 points (CI 2.59 to 17.61). Teacher reports indicated significant differences in arithmetic when outcome was dichotomised to 'below grade' or 'not below grade'. There were no significant associations between outcome measures and the medical or perioperative parameters, however, including those related to hypoxia. It is concluded that the increased incidence of academic problems and the nature of the cognitive difficulties in children with uncomplicated corrective cardiac surgery for cyanotic heart disease are not fully explained by chronic hypoxia, or by other factors related to the cardiac surgery.