Quantitative In situ hybridization and computer-assisted microscopy were used to compare GnRH gene expression in the hypothalamus of premenopausal and postmenopausal women. Hypothalamic sections were incubated with 35S-labeled 48-base complementary DNA probes and dipped into nuclear emulsion for visualization of messenger ribonucleic acids at the single cell level. Two subtypes of GnRH neurons were examined: heavily labeled GnRH neurons located primarily in the medial basal hypothalamus (type I) and lightly labeled neurons in the dorsal preoptic-septal region (type II). We report a 50% increase in mean number of silver grains per type I neuron in the medial basal hypothalamus of postmenopausal women. In contrast to type I neurons, there was no difference in the number of grains per type II neuron in the dorsal preoptic-septal regions. The mean profile area and the number of type I GnRH neurons per section were not different between the two groups, and there was no change in the size of type II neurons. There was also a significant postmortem degradation of messenger ribonucleic acid in type I, but not type II, neurons. We hypothesize that the increase in GnRH gene expression in the medial basal hypothalamus of postmenopausal women is secondary to the ovarian failure of menopause and is not a nonspecific effect of age. The differential response of the two types of hypothalamic neurons provides additional evidence that distinct functional subgroups of GnRH neurons exist in the human brain.