46, XY partial gonadal dysgenesis is a rare condition characterized by a varying degree of testicular dysgenesis, ambiguous genitalia, and usually absence of regression of Müllerian structures. The management of patients with these disorders warrants revisiting, owing to recent molecular biological findings and to reports on the long-term outcome of individuals with ambiguous genitalia. We report on a patient with 46, XY chromosomes, presence of the "sex-determining region of Y chromosome" (SRY) gene, scrotal gonads, fallopain tubes, uterus, vagina, and ambiguous genitalia with a penisoid, perineal hypospadia and sinus urogenitalis. Gonadal biopsy revealed virtually normal testicular tissue in both gonads. Removal of the gonads during surgery for a cystic adnex tumor revealed clear signs of partial gonadal dysgenesis. The decision to raise the child as a male was made by parents and physicians caring for the patient. Administration of testosterone, removal of the uterus and adnexes, in addition to repair of the hypospadia permitted an almost normal penis to be formed with normal male micturition. In the management of affected patients it has to be considered that establishing the diagnosis may be extremely tricky, even with the use of gonadal biopsies. The decision on sex assignment may be even more difficult, since future gender identity, limitations of genital reconstructive surgery and the potential for development of gonadal tumors have to be taken into consideration. While in the past, female sex assignment was commonly recommended for such patients, raising them in a male gender role is now considered. Parents should be involved in the decision that is ultimately based on extensive analysis of the individual case.