We describe a case of the juvenile form of Pompe's disease that presented as primary alveolar hypoventilation due to respiratory muscle involvement. This 17-year-old girl had been asymptomatic until this admission, although she had a delayed puberty. Arterial blood gas analysis, pulmonary function test as well as physical findings were compatible with chronic alveolar hypoventilation syndrome. Since she had lower extremity muscle weakness and pseudomyotonic discharge on electromyography a muscle biopsy was done, which revealed glycogen storage disease. The patient was managed successfully with nasal intermittent positive pressure ventilation.