PURPOSE The majority of known female carriers of X-linked chronic granulomatous disease (X-CGD), a deficiency of the gp91-phox (phagocyte oxidase) subunit and the most common genetic subtype of CGD, are not informative for the linked restriction fragment length polymorphisms (RFLPs) described to date. The isolation and characterization of two polymorphic (CA/GT)n repeats that lie within the X-CGD gene are reported, which are a useful linked marker for prenatal diagnosis. PATIENTS AND METHODS cDNA for gp91-phox was used to probe a genomic library. Genomic clones were isolated and screened for (CA/GT)n repeats. The repeats were isolated and sequences surrounding the repeats were determined. Oligonucleotide primer pairs surrounding the repeats were chosen to facilitate polymerase chain reaction (PCR) across the repeat. RESULTS Analysis of DNA derived from over 100 individuals shows both markers to be highly polymorphic with a resultant high proportion of heterozygosity in females. Several kindreds affected by X-CGD were studied and the (CA/GT)n length polymorphisms were shown to segregate with the clinical syndrome or biochemical carrier status. The technique was prospectively applied to several kindreds containing a carrier mother and an affected child. In a case where a male fetus was shown to carry the unaffected allele, the pregnancy was carried to term and the child was not affected. CONCLUSIONS This approach is highly informative in a multiple allele system, can provide a technical analysis in just hours, requires only a ng of DNA, and permits the transport of diagnostic samples. Therefore, this method can be used early in pregnancy on a chorionic villus biopsy sample for prenatal diagnosis.