Fertilization and development of mouse embryos occur in the ampullae of oviduct. Various growth factors and embryotrophic factors produced by the oviductal cells have been demonstrated to enhance embryo development in vitro. As a step towards understanding the genetic changes of mouse oviduct during mouse embryos preimplantation period, we adopted suppression subtractive hybridization (SSH) to establish four subtracted cDNA libraries to identify (1) oviduct-expressing genes, and (2) genes that may support embryo development in vivo. Using this method, we isolated 82, 88, 99, and 109 clones from four mouse libraries prepared from 0 (day 0), 24 (day 1), 48 (day 2), and 72 h (day 3) post-human chorionic gonadotropin (hCG) treated mice. Reverse dot-blot analysis confirmed that 25 (day 0), 24 (day 1), 40 (day 2), and 29 (day 3) clones were highly expressed in mouse oviduct when compared to other tissues. DNA sequence analysis identified genes encoding mouse oviduct-specific glycoprotein (MOGP), actin-binding protein 280, and several viral genes. Northern analysis confirmed that the genes were mainly expressed in oviduct, with some viral genes also expressed in uterus. About 9% of these oviduct expressing clones (11/118) were novel. We further demonstrated that one of the novel clones ODEG0-17 was expressed in the oviduct during early embryo preimplantation period and rarely in other tissues by RT-PCR. Our results show that SSH is a powerful method applicable to identifying tissue-specific transcripts on fertilization and development.