The molecular basis of a patient with 5alpha-reductase deficiency was investigated in this study. This disease is a rare form of male pseudohermaphroditism with virilization during puberty. The child was raised as a girl, but had a male gender identity early in life. The diagnosis was set at the age of 13 years when the virilization process began. Hypospadias repair was performed and he changed to a male gender. DNA sequence analysis disclosed a homozygous mutation in exon 4 of the 5alpha-reductase type 2 gene, alanine 228 for threonine. The heterozygous parents are first cousins of Pakistani origin.