This article discusses general issues with regard to gender-identity problems, sex reassignment, and clinical management in patients with ambiguous genitalia, based on a detailed case history of a patient with penile agenesis who has been followed more than 20 years. After initial uncertainty, the patient began to grow up as a boy, lived from the fourth year of life as a girl and young woman, and lived from late puberty on as a man. Over his lifetime he experienced extensive corrective surgery plus hormonal substitution therapy. Pre- and perinatal hormonal conditions, phenomenology of the genitalia, sex of rearing, timing of sex reassignment and corrective surgery, for example, appear to be important components for the development of gender-role behavior, gender identity, and sexual orientation of intersex patients. Findings and retrospective considerations for this patient suggest the need for careful differential activities in diagnostic workup, approaches to sex assignment and possible reassignment, and the clinical management of patients and families.