Microangiopathic hemolytic anemia and thrombocytopenia have been reported in patients with primary pulmonary hypertension, but not in patients with congenital heart disease even if accompanied with pulmonary hypertension. We present a 7-year-old boy with atrial septal defect and pulmonary hypertension who developed microangiopathic hemolysis and thrombocytopenia. Microangiopathic hemolytic anemia and thrombocytopenia should be remarked as a complication in patients with congenital heart disease.