We used differential-display reverse transcription-polymerase chain reaction (DDRT-PCR) to identify different patterns of progesterone (P4)-dependent gene regulation in rhesus monkey endometria. Complementary DNA populations representing the proliferative phase (estrogen dominant, EcDNA) and an inadequate secretory phase (low level of P4, IcDNA) were compared with a cDNA population representing an adequate secretory phase (normal level of P4, PcDNA). We were able to distinguish four different levels of mRNA regulation: 1) up-regulation by P4 during an adequate secretory phase, 2) autologous down-regulation (IcDNA versus PcDNA), 3) lower abundance in IcDNA compared to PcDNA, and 4) P4-dependent inhibition of EcDNA gene expression. We isolated and sequenced 16 fragments representing these different levels of P4 regulation. The sequence of three fragments that were autologously down-regulated (I1, I2, I4) matched previously entered GenBank mRNAs: I1 encodes serine/threonine protein phosphatase A; I2 encodes oxobutanoate dehydrogenase E1b-beta; and I4 encodes line-1 reverse transcriptase homologue. Six other fragments exhibited homology to uncharacterized expressed sequence tags, sequence site tags, and cosmid clones. The remaining seven fragments exhibited no significant homology to GenBank entries at this time. The various patterns of P4-dependent gene regulation identified in the present study are likely to play roles in the temporal orchestration of events that lead to proper maturation of the endometrium.