Glycogen-storage disease type II (GSD II, acid maltase deficiency, Pompe's disease) is caused by defects in the lysosomal acid alpha-glucosidase (GAA) gene. Clinically, patients with the severe infantile form of GSD II have muscle weakness and cardiomyopathy eventually leading to death before the age of two years. Patients with the juvenile or the adult form of GSD II present with myopathy with a slow progression over several years or decades. Apart from a common base substitution in intron1, designated IVS1(-13T-->G) and resulting in the aberrant splicing of exon 2, the other mutations recently discovered in the GAA gene are rare and often unique to single patients. In this paper, we identified a two-base frameshift deletion in three unrelated adult-onset GSD II patients. This small deletion lies in the first coding exon (exon 2) and results in a premature stop codon at the very 5' end of the coding sequence of the GAA gene. The three patients were compound heterozygotes and two of them had the common IVS1(-13G-->T) mutation on the second allele. We speculate that this novel deletion may be relatively frequent among French patients, possibly leading to the severe infantile phenotype of GSD II if it occurs in homozygous form.