Two neutral alpha-glucosidase isoenzymes were isolated from the muscle of Japanese quails with late-onset acid maltase deficiency. One isoenzyme is predominantly expressed in embryonic muscle and the other in adult muscle. The time of switching from one to the other of these two neutral alpha-glucosidases was the same as in normal birds. The glycogen content in acid maltase-deficient muscle was not inversely proportional to the amount of embryonic neutral alpha-glucosidase. From the results, we conclude that (i) the transition of neutral alpha-glucosidase from the embryonic to the adult type is not influenced by the disease, and (ii) the embryonic neutral alpha-glucosidase seems not to be directly correlated with glycogen storage in skeletal muscle. In acid maltase-deficient muscle, the activity of the embryonic type began to increase again from 14 days after hatching, and attained a level corresponding to 18% of the total neutral alpha-glucosidase activity at 3 months (P less than 0.025). Its biochemical characteristics were the same as those of the normal embryonic neutral alpha-glucosidase. It should be clarified why the reappearance of the normal embryonic type occurs in acid maltase-deficient adult muscle and whether or not the reappearance of the embryonic neutral alpha-glucosidase represents regenerating muscle.