A 13-year-old boy with the juvenile type of acid alpha-glucosidase deficiency is presented. Muscle CT scans performed before muscle biopsy revealed high image density over the entire rectus femoris, and partial high density over the iliopsoas, adductor magnus and tibialis anterior. MRI of the rectus femoris in the transaxial plane showed high image intensity over the entire length of the muscle in both T1- and T2-weighted images. A biopsy revealed a surprising histological difference between the rectus femoris, which showed pronounced vacuolar myopathy with excessive glycogen, and the vastus lateralis, in which deposition of glycogen was minimal and the CT image indicated a normal muscle density. The findings in this case suggest that CT scanning and MRI are useful in recognizing muscle involvement in acid alpha-glucosidase deficiency, which is characterized by images of increased density compared to normal muscle, presumably because excessive deposition of glycogen and lysosomal membranes cause high X-ray absorption on CT and high signal intensity on MRI.