The highly polymorphic human DXS16 locus on Xp22 contains a BglII restriction fragment length polymorphism with 33% heterozygosity. We report that methylation of the HpaII site, 3.1 kb away from this restriction fragment length polymorphism, correlates with X-inactivation. The BglII polymorphism distinguishes between the maternal and paternal alleles, and HpaII digestion identifies their methylation status. The accuracy of this assay was tested on more than 30 control females and some patients with known patterns of X-inactivation. The data obtained from this assay agree substantially with those obtained using the androgen receptor assay, which is widely used for detecting patterns of X-inactivation. This is the first marker on Xp22 found to be suitable for clonal analysis. Of additional significance is this marker's proximity to the pseudoautosomal boundary on the X chromosome and its potential use in identifying rare events occurring in this region, which lead to escape from normal X-inactivation.