Glycogen storage disease II (GSDII or Pompe disease, OMIM # 232300) is an autosomal recessive hereditary lysosomal disorder. Mutations in the GAA gene usually lead to reduced acid α-glucosidase (acid maltase, GAA, OMIM *606800, EC 3.1.26.2) activity, which results in impaired degradation and subsequent accumulation of glycogen within lysosomes. We present an Iranian boy, who was diagnosed with GSDII based upon clinical and biochemical findings. A single adenine insertion (insA) was detected at codon 693 that leads to a predicted premature stop codon at codon 736 in the GAA gene. The parents were heterozygous for the same change. According to the human genome mutation database (www.hgmd.org) and lecture reviews, the detected change is a novel mutation. We suppose that the discovered insertion in the GAA gene might lead to a reduced activity of the gene product. This assumption is in agreement with biochemical and clinical signs in the patient.