The autopsy findings in a clinically and biochemically documented case of adult‐onset acid maltase deficiency presenting with limb girdle myopathy are presented. The skeletal muscles, tongue, extraocular and smooth muscles of gut and arterioles showed a vacuolar myopathy, most severely affecting proximal skeletal muscles. Muscle spindles were severely affected in all muscles. The heart showed basophilic degeneration and a vacuolar myopathy. The visceral organs and nervous system were morphologically normal. Possible mechanisms for this differential involvement of muscles and tissues are discussed.