Using in situ hybridization histochemistry, we have detected perikarya containing mRNA encoding GnRH and GnRH-associated peptide (GAP) in rat brains. Synthetic DNA oligomers with sequences complementary to the rat cDNA encoding the GnRH structural region and the GAP structural region were hybridized to formaldehyde-fixed coronal sections. The distribution and number of cells containing GnRH/GAP mRNA were similar to those shown by immunocytochemical studies. The areas in which GnRH mRNA perikarya were shown included the medial septal area, the diagonal band of Broca, the preoptic area, and the anterior hypothalamus. Up to 55 cells were detected in a single 12-micron section containing the diagonal band and organum vasculosum lamina terminalis (OVLT) whereas cell numbers diminished in more caudal regions. In addition, both probes labeled the same cells contained within adjacent sections. We used this technique to examine the effect of estrogen on GnRH mRNA levels in the area of the OVLT of normal and androgen-sterilized female rats, using an estrogen treatment paradigm previously characterized in studies investigating the hypothalamic regulation of negative and positive estrogen feedback. We found that 7 days after ovariectomy, 2 days of estrogen treatment resulted in a significant reduction in the average cellular level of GnRH mRNA in both normal and androgen-sterilized females. Analysis of histograms relating the intensity of labeling to the abundance of cells suggested that a small population of GnRH cells responded to the estrogen treatment. However, we found no evidence for a discrete neuroanatomical segregation of such a subpopulation of GnRH-responsive cells within the area of the OVLT.