Glycogen storage disease type II is an autosomal recessive disorder of glycogen metabolism due to deficiency of lysosomal acid alpha-glucosidase. We present the molecular and enzymatic analyses of 22 Spanish GSD II patients. Molecular analyses revealed nine novel mutations. The most common defects were mutations c.-32-13T>G (25%) and c.1076-1G>C (14%) and we report the first homozygous patient for c.1076-1G>C mutation presenting with an infantile form. Alleles bearing mutation c.-32-13T>G are associated with the same haplotype.