We describe a girl of 12.7 years who had GnRH deficiency after surgery and radiotherapy for a craniopharyngioma at age 5 years. She had large cystic ovaries with a small uterus in the absence of spontaneous gonadotropin pulsatility. Puberty was induced by low-dose pulsatile GnRH treatment over a 1.5-year period. In the perimenarcheal period, ovarian morphology became typical of PCO with abnormal diurnal pulsatile gonadotropin secretion. These data suggest that PCO is primarily a disorder of the ovary and that the observed gonadotropin abnormalities are secondary to the ovarian lesion.