A rare case of pulmonary hypertension due to glycogen storage disease type II (Pompe's disease) was reported. An 18-year-old girl was admitted to Kawasaki Medical School Hospital because of cyanosis, dyspnea on exertion and amenorrhea. She was 149 cm in height and 29 kg in body weight. Clinical examination revealed that pulmonary artery pulse and right ventricular heave were palpable over the precordium. On auscultation, an accentuated pulmonic second heart sound, pulmonic ejection sound and diastolic decrescendo murmur (Levine III/VI) were heard in the second intercostal space at the right sternal border. Her skeletal muscles, especially her intercostal muscles were generally weak and atrophic. Her electrocardiogram showed a pulmonary P-wave and right ventricular hypertrophy. The chest X-ray revealed right ventricular enlargement and a dilated pulmonary trunk. On echocardiography, the right ventricle and the main pulmonary artery were dilated, and a systolic notch of the pulmonary valve was found. Swan-Ganz catheterization disclosed that pulmonary artery pressure, right ventricular pressure and mean pulmonary capillary wedge pressure were 76/35 (50) mmHg, 76/12 mmHg and 10 mmHg, respectively. Respiratory function tests showed severe restrictive ventilatory impairment with hypercapnea and hypoxemia. On biopsy of the left quadriceps femoris muscle, the most striking finding was numerous intracytoplasmic vacuoles. The small vacuoles were stained with PAS and acid phosphatase. Electron microscopy showed massive glycogen accumulation in the sarcoplasm and membrane bound vacuoles (glycogenosome). Alpha-1, 4-glucosidase activity in the peripheral lymphocytes was definitely decreased. Her pulmonary hypertension resulted from respiratory muscular atrophy and alveolar hypoventilation caused by Pompe's disease.