Late-onset acid maltase deficiency or glycogen storage disease type II (GSD II) is a rare disorder of intralysosomal glycogen metabolism, resulting in progressive myopathy that is secondary to increased muscle protein breakdown. Stable isotope studies in the postabsorptive state have confirmed that mean protein breakdown in GSD II is increased by 31% compared to control subjects. 6.86 versus 4.69 g/kg per day, that mean protein balance is reduced is GSD II -1.32 versus -1.06 g/kg per day. Indirect calorimetry has demonstrated an increase in mean resting energy expenditure in GSD II, 41.8 versus 31.2 kcal/kg per day. Compliance following the introduction of a high-protein diet is often poor due to the large quantities of protein necessary and to the high caloric intake with the consequent weight gain. Only 25% of all reported subjects with GSD II showed an improvement of muscle or respiratory function after a high-protein diet. Careful evaluation of the underlying pathophysiological changes in GSD II is necessary to develop more logical and therefore more beneficial forms of dietary treatment.