Lenz microphthalmia syndrome is an extremely rare inherited disorder, characterized by unilateral or bilateral microphthalmia. In rare cases affected patients exhibit complete absence of eye or blepharoptosis resulting in visual impairment. Additional physical abnormalities are often associated with this disorder, orofacial, digital, skeletal and urogenital abnormalities. Here we present three cases of Lenz microphthalmia with additional manifestations: two brothers of first cousin mating, the elder one has bilateral congenital cataract which is a rare ophthalmological finding in this syndrome and a third case who presented to us because of ambiguous genitalia. She was 12 years old, and reared as a female. Chromosomal analysis showed 46,XY karyotype, and hormonal studies indicated 5-alpha reductase deficiency. This is the first report of the association of 5-alpha reductase deficiency with Lenz microphthalmia syndrome.