Properties of the acid alpha-glucosidase, GAA2, the product of the GAA*2 allele have been compared with those of the common allele product GAA1, GAA2 has an altered affinity for glycogen but resembles GAA1 in its affinity for low molecular weight substrates, and also in its processing, as judged by immunoblot analysis of the denatured polypeptides. Starch gel electrophoretic analysis of fibroblasts from 15 patients with late onset glycogen storage disease type II (GSDII) failed to reveal either homozygotes or heterozygotes for the GAA*2 allele (GAA2-2 or GAA2-0) providing evidence that neither of these genotypes lead to late onset GSDII despite the impaired activity of the enzyme towards glycogen.