The steroid 5 alpha-reductase type II enzyme catalyzes the conversion of testosterone (T) to dihydrotestosterone (DHT), and its deficiency leads to undervirilization in 46, XY individuals, due to an impairment of this conversion in genital tissues. Molecular analysis in the steroid 5 alpha-reductase type II gene (SRD5A2) was performed in two 46, XY female siblings. SRD5A2 gene sequencing revealed that the patients were homozygous for p. Gln126Arg missense mutation, which results from the CGA > CAA nucleotide substitution. The molecular result confirmed clinical diagnosis of 46,XY disorder of sex development (DSD) for the older sister and directed the investigation to other family members. Studies on SRD5A2 protein structure showed severe changes at NADPH binding region indicating that structural modeling analysis can be useful to evaluate the deleterious role of a mutation as causing 5 alpha-reductase type II enzyme deficiency.