The autosomal recessive disorder Glycogen Storage Type II (GSDII) is caused by a deficiency in the lysosomal enzyme acid alpha-glucosidase. We have optimised a procedure to use fluorescent DNA sequencing technology to screen for mutations within the alpha-glucosidase gene from UK patients with GSDII. Five previously unknown mutations in six patients (4 early onset infantile and 2 late adult) have been found. The mutations are an insertion of a C residue in exon 2 (InsC258), an insertion of a G residue in exon 16 (InsG2242), a deletion of 20 nucleotides in exon 4 delta, and a nonsense mutation in exon 16 (G2237A-Trp746Stop). All will result in the introduction of a premature stop codon in the coding region, predicting a truncated and non-functional protein. The final mutation is a duplication of 18 nucleotides in exon 19 (Ins18nt2776) and will result in the insertion of an additional six amino acids into the protein chain after Asn925 (Gly-Val-Pro-Val-Ser-Asn).