Pompe disease is an uncommon autosomal recessive glycogen storage disorder 
caused by deficiency of acid α-glucosidase. Classic infantile form triggers 
severe cardiomyopathy, hypotonia, and respiratory failure, leading to death 
within the first two years of life. The majority of patients with Pompe disease 
have been reported to have point mutations in the GAA gene. We report the first 
complex deletion-insertion encompassing the complete structure of GAA gene and a 
large fragment of the gene CCDC40 in a patient with very severe form of Pompe 
disease. Sequencing analysis of breakpoints allowed us to determine the 
potential implication of an Alu repeat in the pathogenic mechanism. We suggest 
that molecular strategy of Pompe disease should include systematic analysis of 
large rearrangements.