Glycogen storage disease type II Pompe (GSD II) is a lysosomal storage disease caused by an inherited deficiency of acid alpha-glucosidase. In addition to the classical infantile form of GSD II, several clinical variants are known. We describe an infant with the classical course of the disease. Our patient differs from the classical variant by the lack of cardiomegalia and the high residual activity of acid alpha-glucosidase in cultivated skin fibroblasts and muscle tissue. In the present case, however, glycogen storing lysosomes were found in peripheral lymphocytes and skeletal muscle cells. This finding underlines the particular value of ultrastructural investigation in the diagnosis of GSD II.