Guidelines for the prevention and management of infective endocarditis (IE) in children with congenital heart disease (CHD) have not been established, so the aim of this study was to clarify the incidence, practical prevention and management of IE in patients with CHD in Japan through a nationwide survey. A written questionnaire was sent to members of the Japanese Society of Pediatric Cardiology and Cardiac Surgery and information was obtained from 236 cardiologists in 228 institutions. Four hundred and eight patients with IE were hospitalized during 1997 to 2001 (1/173 admissions with CHD including those hospitalized for cardiac catheterization or surgery). Prevention of IE for CHD was undertaken by 92% of cardiologists, usually oral penicillins (73%) and less frequently cephems (18%) were prescribed. The Duke criteria were used as clinical criteria by 38%. Blood culture was performed once only by 40%. Penicillins and aminoglycosides (38%) were frequently administered for management of culture-negative IE. There were variations in the dose and duration of antibiotics for prevention and management of IE. It appears that the prevalence of IE in CHD is rising and the nationwide survey revealed more variations in practical prevention and management of IE in patients with CHD than expected. The results should be helpful in making future guidelines for management of IE in CHD.