Two mutations in the lysosomal alpha-glucosidase gene, a single base pair deletion (delta T525) and a deletion of exon 18, have recently been identified with a relatively high incidence in Caucasian patients with glycogen storage disease type II (GSD II). Prenatal diagnosis was made in a pregnancy of consanguineous parents of a child with GSD II. The delta T525 deletion was demonstrated in this family but unexpectedly in only one of the parents. The absence of the delta T525 deletion in DNA isolated from the chorionic villi and a normal alpha-glucosidase activity indicated that the fetus was not affected. The possible role of mutation analysis in the prenatal diagnosis of GSD II is discussed in the light of our previous experience from a series of 100 prenatal diagnoses for this disorder by enzyme analysis.