Abstract. We performed the first genome-wide expression analysis to compare the differences in gene expression in the female sperm reservoir of the duck reproductive tract between two groups with long and short fertile periods to identify factors that may be associated with the fertile period using an oligonucleotide microarray. RNA was extracted from the uterovaginal junction (UV junction) of the two groups. Affymetrix chips containing comprehensive coverage of 32773 transcripts were hybridized with biotin-labeled cRNA, and three biological repeats were performed. We identified 27 transcripts as being differentially regulated. Interestingly, by mapping the differentially expressed transcripts to annotated pathways, we found that Neuropeptide Y (NPY), the RNA expression of which was increased by 2.96-fold in the short-fertile-period group as compared with the long-fertile-period group in our experiment, has been shown to reduce blood flow and substance supply to local tissues. Enah/Vasp-like (EVL), the RNA expression of which was significantly increased by 1.77-fold in the short-fertile-period group as compared with the long-period group, has been demonstrated to be important in activated T-cells. In contrast, trafficking kinesin-binding protein 1 (TRAK1), the expression of which was increased by 2.33-fold in the long-period group as compared with its counterparts, has been suggested to inhibit precocious activation of sperm and prolong sperm life in the female sperm reservoir. The results of real-time PCR confirmed the data obtained by microarray analysis. Our study demonstrated that combining global gene expression investigation with annotated pathway resources contributes to the understanding of sperm life when sustained in the UV junction.Key words: Differentially expressed transcripts, Duck, Fertile period, Uterovaginal junction (J. Reprod. Dev. 57: [731][732][733][734][735][736] 2011) A fter the entry of sperm into a female genital tract before ovulation, sperm accumulate to a certain amount and are stored in the female sperm reservoir [1], which is a widespread phenomenon among numerous avian, reptilian and mammalian species [2][3][4]. The sperm reservoir then releases sperm gradually for successful fertilization after a single insemination, the period of which varies from hours to weeks in different species [2,[4][5][6]. This period is defined as the fertile period. A long fertile period means prolonged sperm survival and leads to a high fertilization rate [7].The process of sperm migration in the female genital tract is more than simply transportation from the position of insemination to the position of fertilization. Rather, it is a complex continuum: entry into the lower genital tract, defense against the tract environment and immunological response, retention in the storage reservoir, activation, taxiing of activated sperm towards oocytes [8], and phagocytosis of nonfertilizing sperm. During sperm storage in the reservoir of the female reproductive tract, there is a close interaction between sperm...