Estradiol accelerates oviductal embryo transport in the rat through changes of genomic expression in oviductal cells. However, the genes involved are unknown. We used a differential display by reverse transcription-polymerase chain reaction to detect estradiol (E2)-dependent genes in the rat oviduct. Rats on day 2 of pregnancy were untreated or treated with 10 µg of E2 and the oviducts were extracted at 30, 180 and 360 min later and used to isolate RNA. Products of reverse transcriptase-PCR, made with pairs of arbitrary and oligo-deoxythymidine primers, were separated on denaturing polyacrylamide gels and candidate bands were excised and reamplified. Truly positive cDNA fragments determined by a single strand conformation polymorphism assay were cloned and sequenced. A ribonuclease protection assay confirmed that clone 25 is up-regulated by E2 in the oviduct at 30, 180 and 360 min. This clone exhibited no homology with known genes and in situ hybridization showed it is only expressed in the epithelial cells of the isthmic segment. Clone 25 is likely to represent a new gene, which is up-regulated by E2 in the epithelium of the isthmic segment of the rat oviduct. Its time frame of response is compatible with a mediator of the effect of E2 on oviductal embryo transport