Mutations in the androgen receptor (AR) gene result in a wide range of phenotypes of the androgen insensitivity syndrome (AIS). Inter- and intrafamilial differences in the phenotypic expression of identical AR mutations are known, suggesting modifying factors in establishing the phenotype. Two 46,XY siblings with partial AIS sharing the same AR gene mutation, R846H, but showing very different phenotypes are studied. Their parents are first cousins. One sibling with grade 5 AIS was raised as a girl; the other sibling with grade 3 ALS was raised as a boy. In both siblings serum levels of hormones were measured; a sex hormone-binding globulin (SHBG) suppression test was completed; and mutation analysis of the AR gene, Scatchard, and SDS-PAGE analysis of the AR protein was performed. Furthermore, 5 alpha -reductase 2 expression and activity in genital skin fibroblasts were investigated, and the 5 alpha -reductase 2 gene was sequenced. The decrease in SHBG serum levels in a SHBG suppression test did not suggest differences in androgen sensitivity as the cause of the phenotypic variation. Also, androgen binding characteristics of the AR, AR expression levels, and the phosphorylation pattern of the AR on hormone binding were identical in both siblings. However, 5 alpha -reductase 2 activity was normal in genital skin fibroblasts from the phenotypic male patient but undetectable in genital skin fibroblasts from the phenotypic female patient. The lack of 5 alpha -reductase 2 activity was due to absent or reduced expression of 5 alpha -reductase 2 in genital skin fibroblasts from the phenotypic female patient. Exon and flanking intron sequences of the 5 alpha -reductase 2 gene showed no mutations in either sibling. Additional intragenic polymorphic marker analysis gave no evidence for different inherited alleles for the 5 alpha -reductase 2 gene in the two siblings. Therefore, the absent or reduced expression of 5 alpha -reductase 2 is likely to be additional to the AIS. Distinct phenotypic variation in this family was caused by 5 alpha -reductase 2 deficiency, additional to AIS. This 5 alpha -reductase deficiency is due to absence of expression of the 5 alpha -reductase iso-enzyme 2 as shown by molecular studies. The distinct phenotypic variation in AIS here is explained by differences in the availability of 5 alpha -dihydrotestosterone during embryonic sex differentiation.