Background: Implantation is a complex process that requires a delicate cooperation between the immune and reproductive system. Any interference in the fine balance could result in embryo loss and infertility. We have recently shown that Toll-like receptor 5 activation results in a decrease of trophoblast cells binding to endometrial cells in an in vitro model of human implantation. However, little is known about the downstream signalling leading to the observed failure in implantation and the factors that modulate this immune response. Methods and Principal Findings: An in vitro model of embryo implantation was used to evaluate the effect of trophoblasts and flagellin on the activation of NF-kappa B in endometrial cells and whether TLR5-related in vitro implantation failure is signalled through NF-kappa B. We generated two different NF-kappa B reporting cell lines by transfecting either an immortalized endometrial epithelial cell line (hTERT-EECs) or a human endometrial carcinoma cell line (Ishikawa 3-H-12) with a plasmid containing the secreted alkaline phosphatase (SEAP) under the control of five NF-kappa B sites. The presence of trophoblast cells as well as flagellin increased NF-kappa B activity when compared to controls. The NF-kappa B activation induced by flagellin was further increased by the addition of trophoblast cells. Moreover, blocking NF-kappa B signalling with a specific inhibitor (BAY11-7082) was able to restore the binding ability of our trophoblast cell line to the endometrial monolayer. Conclusions: These are the first results showing a local effect of the trophoblasts on the innate immune response of the endometrial epithelium. Moreover, we show that implantation failure caused by intrauterine infections could be associated with abnormal levels of NF-kappa B activation. Further studies are needed to evaluate the target genes through which NF-kappa B activation after TLR5 stimulation lead to failure in implantation and the effect of the embryo on those genes. Understanding these pathways could help in the diagnosis and treatment of implantation failure cases.