An abnormal 2.3 kb SacI fragment of the human lysosomal alpha-glucosidase gene (GAA) was identified in patients with glycogen storage disease type II. The fragment results from deletion of exon 18 and adjacent parts of intron 17 and 18. The borders of the deletion are marked by the occurrence of an eight nucleotide long tandem repeat (AGGGGCCG) which is apparently instrumental in the mutation event. The exon 18 deletion was demonstrated in 10 out of 39 patients from Europe (all hetero-allelic) and is so far the most common mutation in this disease (allele frequency among patients is 0.13).