Glycogen Storage Disease Type II (GSDII) is a recessively inherited disorder due to the deficiency of acid alpha-glucosidase (GAA) that results in glycogen accumulation in the lysosomes. The molecular analysis of the GAA gene was performed on 45 Italian patients with late onset GSDII. DHPLC analysis revealed 28 polymorphisms spread all over the GAA gene. Direct sequencing identified the 96% of the mutant alleles, 12 of which are novel. Missense mutations were functionally characterized by enzyme activity and protein processing in a human GAA deficient cell line while splicing mutations were studied by RT-PCR and in silico analysis. A complex allele was also identified carrying three different alterations in cis. All the patients studied carried a severe mutation in combination with a milder one, which explains the late onset of the disease. The c.-32-13T > G was the most frequent mutation, present as compound heterozygote in 85% of the patients as described in other late onset GSDII Caucasian populations. Interestingly, 10 of the 45 patients carried the c.-32-13T > G associated to the severe c.2237G > A (p.W746X) mutation. However, despite the common genotype, patients presented with a wide variability in residual enzyme activity, age of appearance of clinical signs and rate of disease progression, suggesting that other genetic/environment factors may modulate clinical presentation.