The importance of the role of acid alpha-glucosidase in the lysosomal degradation of glycogen has been emphasized because the deficiency of this enzyme in glycogenosis type II causes glycogen accumulation in lysosomes. Three clinical variants are distinguished. The infantile type has its onset shortly after birth and is known as generalized glycogen storage disease. The adult variant manifests itself mostly after the second decade of life and is characterized by progressive skeletal muscle weakness. The other is childhood type which is usually fatal by the second decade of life. Many biochemical reports of acid alpha-glucosidase have been published. Martiniuk et al reported the cDNA and amino acid sequence of human acid alpha-glucosidase. In prior studies, they reported that the lysosomal acid alpha-glucosidase was polymorphic with three alleles. The rarer allele GAA2 allozyme had a lower affinity for glycogen and starch. We also reported the enzyme heterogeneity in its affinity to Sephacryl S-200 gel. Whereby the enzyme separated into two fractions, S1 and S2. Each fraction contained 76 kDa and 67 kDa components on SDS/PAGE. The spleen enzyme consisted mainly of S1 fraction, containing only a 76 kDa component. In previous extensive studies, different mutations of Pompe's disease have been inferred from alterations in biochemical parameters. More recently Martiniuk et al, Hoefsloot et al and Van der Ploeg et al reported the analysis of cDNA and mRNA. These studies have revealed an absence or abnormal size of mRNA in large numbers of patients and altered restriction endonuclease fragments in a few patients.(ABSTRACT TRUNCATED AT 250 WORDS)