Establishment and maintenance of pregnancy in the pig involves intricate communication between the developing conceptuses and maternal endometrium. Conceptus synthesis and release of estrogen during trophoblastic elongation is an essential factor involved with establishing conceptus-uterine communication. The present study identified endometrial changes in gene expression associated with implantation failure and complete pregnancy loss following premature exposure of pregnant gilts to exogenous estrogen. Gilts were treated with either 5 mg estradiol cypionate (EC) or corn oil (CO) on D 9 and D 10 of gestation, which was associated with complete conceptus degeneration by D 17 of gestation. Microarray analysis of gene expression revealed a total of 8, 32 and 5 genes were up-regulated in the EC endometrium, while 1, 39, and 16 genes were down-regulated, on D 10, 13 and 15, respectively. Four endometrial genes altered by EC; aldose reductase (AKR1B1), secreted phosphoprotein 1 (SPP1), CD24 antigen (CD24) and neuromedin B (NMB), were evaluated using quantitative RT-PCR and in situ hybridization. In situ hybridization localized gene expression for NMB, CD24, AKR1B1 and SPP1 in the luminal epithelium and confirmed the expression patterns from RT-PCR analysis. The aberrant expression patterns of endometrial AKR1B1, SPP1, CD24, and NMB 3 to 4 days following premature estrogen exposure to pregnant gilts may be involved with conceptus attachment failure to the uterine surface epithelium and induction of endometrial responses that disrupt the establishment of a viable pregnancy.