Atrial flutter occurs most often in patients with organic heart disease. It appears that chronic atrial flutter is associated with a remarkably high risk of clinically apparent thromboembolism and effective anticoagulation appears to reduce this risk, but acute or recent onset, postoperative atrial flutter may have a lower risk of thromboembolism than those with chronic atrial flutter. In chronic atrial flutter or fibrillation with organic heart disease, anticoagulation is generally justified but there is some debate about anticoagulation in paroxysmal atrial flutter. The spontaneous echo contrast is generally accepted one of the major risk factor of thromboembolism and usually occurred in mitral stenosis, dilated cardiomyopathy, and enlarged left atrium, but rarely observed in apical hypertrophic cardiomyopathy. We experienced a patient with apical hypertrophic cardiomyopathy, who visited to emergency medical center due to dizziness and suffered from cerebral thromboembolism after restoration of sinus rhythm. In transesophageal echocardiography, there was moderate to severe spontaneous echo contrast in left atrium. This patient showed that transesophageal echocardiography evaluation of left atrium might be mandatory in patients with paroxysmal atrial flutter and organic heart disease.