Glycogen storage diseases are a heterogeneous group of metabolic disorder affecting multiple organ system: liver, skeletal muscle, heart and brain. Clinical features include: short status, hepatomegaly, hypoglycemia, dyslipidemia and rare involvement of the myocardium except in the case of type III, glycogen storage diseases with hypertrophic cardiomyopathy in adult, which is extremely rare. We treated a case of hypertrophic cardiomyopathy with hepatomegaly that was unknown etiology. The patient was diagnosed as having glycogen storage disease. This 46-year old women was transferred with dyspnea on exertion and abnormal LFTs. She was diagnosed with hypertrophic cardiomyopathy by echocardiography but there was no specific cause for hypertrophic cardiomyopathy. A liver biopsy was performed. The result showed glycogen storage disease possible type III, IV or IX. In conclusion, patients with hypertrophic cardiomyopathy of unknown etiology and abnormal LFTs should be evaluated for glycogen storage disease.