Pompe disease, also known as glycogen storage disease type II, is caused by acid maltase deficiency, and can lead to lysosomal glycogen storage. The primal manifestations may be observed in children and adults, and also in infants. In general, the clinical spectrum in infants is more progressive and lethal than that in older patients. This case report describes the case of a newborn who was found to have cardiac hypertrophy, hepatomegaly and elevated serum enzyme levels, which was characterized by an aspartate aminotransferase level of 95 U/l, lactate dehydrogenase level of 778 U/l and creatine kinase level of 1,299 U/l. On the basis of the clinical signs and laboratory results, dried blood spots from the baby were tested to determine the acid α-glucosidase (GAA) activity, and the result confirmed that the GAA activity was only 0.10 pmol/punch/h (normal reference range, 2.88-89.02 pmol/punch/h) at pH 3.8, which was clearly lower than the normal range, leading to a diagnosis of Pompe disease. Pompe disease is incurable, and before the introduction of enzyme replacement therapy (ERT), pain relief was the main treatment. Recognizing this disease earlier and starting ERT in infants prior to the development of clinical symptoms is likely to improve the quality of life of patients.