Estrogen prepares the uterus for implantation and is highly conserved in mammals. However, administration of estrogen to pigs earlier than normal conceptus secretion is characterized by complete embryonic mortality by days 15-18. The objective of this study was to characterize the direct effects of early estrogen administration on uterine endometrial gene expression. The study evaluated the effects of estrogen when administered early on days 9 and 10 of the estrous cycle or day 11.5 which is the normal period of conceptus estrogen secretion in pigs. Uterine endometrium was removed either Day 13 or 15. Endometrial gene expression was evaluated using the GeneChip(®) Porcine Genome Array. Fifty-five candidate genes were successfully identified as differentially expressed due to aberrant estrogen exposure, and quantitative RT-PCR mRNA expression was supportive of the array data. These data provide insight into global uterine transcriptional changes associated with estrogen disruption of the endometrium.