Background Studies on microorganisms in a large cohort of patients with congenital heart disease (CHD) and infective endocarditis (IE) are rare. Using a nationwide survey, the relationship between causative microorganisms and clinical profiles in patients with CHD and IE was investigated. Methods and Results Data from 188 patients with CHD (pediatric patients (n=113), mean age, 6.2±4.9 years; adult patients (n=75), mean age 28.4±13.4 years) and IE from 60 institutions were analyzed. Causative microorganisms were Streptococcus species (94:50.0%), Staphylococcus species (68:36.2%), Haemophilus species (9:4.8%), Candida (5:2.7%), Pseudomonas species (4:2.1%) and other unclassified microorganisms (8:4.3%). Staphylococcal IE was observed significantly higher in perioperative IE (11/16), in cyanotic patients (32/73) and patients younger than 1 year old (11/16). Streptococcal IE was observed significantly higher in acyanotic patients (64/109) and patients aged 16 years or older (48/75). Total mortality was 20/188 (10.6%) and was high for candidial (2/5; 40%) and pseudomonal IE (2/4; 50%). Mortality was highly associated with younger age, especially infants (5/16), and methicillin-resistant staphylococcal IE (6/15). Conclusions The causative microorganisms are significantly related to the clinical profile and outcome in patients with IE and CHD. These results form the basis for selecting appropriate antibiotics for prevention and management. (Circ J 2005; 69: 1266 - 1270)