A new method is described for detection of mutations in the lysosomal alpha-glucosidase gene (GAA) leading to Glycogen Storage Disease type II (GSDII). A key feature of the method is isolation and reverse transcription of mRNA followed by PCR amplification of lysosomal alpha-glucosidase cDNA with M13-extended primers. Dye labeled primers are used for cycle sequencing and an ABI PRISM 377 DNA sequencing system for analysis. The method is rapid and complementary to the automated sequencing of all the 19, PCR amplified, coding exons of the GAA gene. The advantages and pitfalls of this new method are discussed in the light of the results obtained with an infantile GSDII patient. A new splice site mutation in the GAA gene of this patient was identified, IVS16(+2T-->C), resulting in the deletion of 16 base pairs of exon 16.