Pompe disease is an autosomal recessive disorder, caused by acid alpha-glucosidase deficiency, which limits the lysosomal breakdown of glycogen, causing accumulation in muscle tissue. Pompe patients suffer from fat replacement of muscle tissue and muscle atrophy, leading to muscle weakness. MRI studies have shown a characteristic pattern with fat replacement of the axial muscles (latissimus dorsi, paraspinal muscles and psoas) and the hamstrings (especially semimembranosus), while distal muscles, and muscles of the anterior thigh compartment are less affected. The aim of this study is to investigate if higher levels of muscle glycogen precede the fat replacement of muscles in Pompe disease. We used C13 NMR spectroscopy at 7 Tesla, to measure the total glycogen value in four muscle groups; the lumbar muscles, the anterior compartment of the thigh, the hamstrings and the calf. The fat-free muscle volume was found using T1 and Dixon sequences and the glycogen concentrations were determined as the total glycogen levels divided by the fat-free muscle volume of distribution. Young Pompe patients with relatively preserved muscles and healthy controls were included. Preliminary results from the first two patients show a higher glycogen concentration in the lumbar and hamstring muscles than in the anterior compartment of the thigh and the calf. Compared to the calf, the glycogen concentration was about fifty percent higher in the lumbar muscles, and twice as high in the hamstrings. Hamstrings had twice as high glycogen levels compared to the anterior compartment of the thigh. Compared to eight healthy controls, the glycogen concentration was 2-3 times higher in all muscle groups of the patients. No clear pattern of muscle glycogen distribution was seen in the control group. These preliminary results indicate a link between high levels of glycogen accumulation in muscle tissue and the subsequent late pattern of fat replacement in Pompe diseases. This is important for the understanding of pathogenesis of muscle wasting in Pompe disease, but could also be an important biomarker for treatment success.