We report a case of infective endocarditis of the mitral valve, which was accompanied by pulmonary emboli traveling through an atrial septal defect. An 18-year-old male was admitted to our hospital due to a fever, polyarthritis and subcutaneous hemorrhage. Transthoracic echocardiography revealed a mobile mass and possible vegetation lodged in the mitral valve and a secundum-type atrial septal defect. Computed tomography revealed a hepatic, splenic and renal embolic infarction. During antibiotic therapy, he felt a sudden right flank pain. Follow-up computed tomography revealed a pulmonary embolic infarction that drifted through an atrial septal defect. This association is the first report, of pulmonary emboli which migrated through an atrial septal defect from the mitral valve.