OBJECTIVE To assess the changing profile of infective endocarditis in patients with congenital heart disease. METHODS All cases diagnosed from 1966 to 2001 (revised Duke criteria) were retrospectively reviewed and categorised in periods I (< 1990) and II (>or= 1990). RESULTS 153 episodes occurred, 81 in period I and 72 in period II. Mean age of affected patients was higher in period II. Non-operated ventricular septal defect, Rastelli correction and palliated cyanotic heart disease increased. Infective endocarditis in corrective surgery changed to patients with prosthetic material. Post-surgical cases decreased. Dental problems were the leading cause (period I 20% v II 33% of cases) with a large variety of pathological organisms (multiple species of Streptococcus). Cutaneous causative infections increased (5% to 17%) with different species of Staphylococcus. Negative blood cultures lessened (20% to 7%, p = 0.03). Streptococci were the most common causative organisms in both periods. Severe heart failure and cardiac complications lessened (20% to 4% and 31% to 18% during periods I and II, respectively). Early surgery was more frequent in period II (32% v 18.5%, p = 0.02). One- and 10-year survival was 91% v 97% in period I and 89% v 97% in period II, respectively (NS). CONCLUSIONS Current targets include complex cyanotic disease, congenital heart disease corrected with prosthetic material and small ventricular septal defect. Postoperative cases lessened; dental and cutaneous causes increased. Survival was unchanged. Prophylactic measures targeted at dental and cutaneous sources should be emphasised.