To characterize the endocrine response during induction of ovulation in patients with hypogonadotropic hypogonadism and ultrasound findings of polycystic ovary, we performed a retrospective analysis of 22 treatment cycles with pulsatile gonadotropin-releasing hormone (GnRH) in such patients and of 17 treatment cycles in similar patients with ultrasonographically normal ovaries. Of the 21 patients studies, 11 had an ultrasound finding of polycystic ovaries and ten had ovaries that appeared normal. Serum luteinizing hormone (LH), follicle-stimulating hormone (FSH) and estradiol levels, number of follicles of diameter > 12 mm (by ultrasound), and ovulation and conception rates were measured. Patients with hypogonadotropic hypogonadism and ultrasound-diagnosed polycystic ovary had pretreatment endocrine status similar to those with normal ovaries, but had much higher baseline ovarian volume. Ovulation induction with pulsatile GnRH induced much higher serum LH concentrations in the former group despite similar FSH levels. This difference preceded any change in estradiol levels. The former group consistently recruited significantly more follicles during pulsatile GnRH treatment. However, ovulation and conception rates were (non-significantly) higher in the latter group. In conclusion, this study characterized a subgroup of hypogonadotropic patients with ovarian morphology, volume and response to ovulation induction similar to in patients with polycystic ovary syndrome. When treated with pulsatile GnRH, those with polycystic ovary significantly hypersecreted LH before their estradiol level changed significantly. The primary lesion in polycystic ovary syndrome seems to be in the ovary, with pituitary hypersecretion of LH secondary to disturbed ovarian feedback signalling.