A recent study has shown that cryptogenic stroke can occur even in patients with small or insignificant atrial septal defects (ASD). However, clinical experience in this field is still limited in Japan, also the efficacy and safety of catheter closure of such defects have not been identified. To evaluate the efficacy and safety of catheter closure of interatrial communication in patients with cryptogenic stroke, 13 patients who were diagnosed with cerebrovascular events due to cryptogenic embolism were included in this study. Mean age at procedure was 43 ± 15 (range 17–68) years. In all patients, the presence of spontaneous or provoked interatrial right-to-left shunts was demonstrated by transesophageal contrast echocardiography. Mean defect size evaluated by the balloon sizing technique was 9.2 ± 2.8 mm, and mean size of the Amplatzer Septal Occluder deployed was 9.5 ± 2.8 mm. Devices were successfully deployed in all patients, though one device migrated into the descending aorta was retrieved by a snare catheter. Complete closure was detected by transesophageal contrast echocardiography at 12 months after the procedure was in 11 (85%) of the 13 patients. During the follow-up period (30.1 ± 9.4 months), no recurrent thromboembolic event was observed. Catheter closure of interatrial right-to-left communications can be safely performed. This procedure may contribute to reduction or prevention of recurrent neurological events in this patient population.