It has been hypothesized that GnRH or a GnRH-like peptide is produced in the rat ovary, but the presence of GnRH in the ovary has not been unequivocally demonstrated. This study was undertaken to determine whether the GnRH gene is expressed in the rat ovary and to compare the GnRH gene transcripts from the ovary and the hypothalamus. Twelve samples of total RNA from ovaries of individual rats were screened by reverse transcription-polymerase chain reaction (RT-PCR) for the presence of GnRH gene transcripts. Fragments of GnRH cDNA were amplified using pairs of specific primers. GnRH transcripts were detected in all the ovaries examined, and differed from hypothalamic GnRH transcripts in two ways: first, in the ovaries a greater proportion of GnRH transcripts contained intronic sequences; second, the major transcription start utilized in the ovary differed from that used in the hypothalamus. Although fully processed GnRH gene transcripts were detected by RT-PCR in both, ovary and hypothalamus, they were not detected in the ovary by Northern blot. The GnRH probe hybridized specifically to the predicted 0.6 kb transcript in the hypothalamus, and to a 3.3 kb transcript in the ovary. We conclude that in the ovary, most GnRH gene transcripts retain intronic sequences.