We have demonstrated up-regulation of the immunomodulatory genes decay accelerating factor (DAF), interleukin 15 (IL-15) and osteopontin (OPN) during the window of implantation (WOI). Here, we characterized gene expression and determined the localization of their protein products and respective ligands at the opening and closure of the WOI. In addition, we used laser capture microdissection (LCM) to analyze the cell type-specific gene expression. Human endometrial biopsies from cycle Days 16, 21 and 24 were evaluated by real-time RT-PCR. Purified epithelial and stromal cells were obtained by LCM. Localization of the proteins and their ligands was assessed by immunohistochemistry. mRNA expression of DAF, IL-15 and OPN was significantly increased throughout the WOI. DAF, OPN and alpha(v)beta(3) integrin were strongly immunolocalized to the glandular compartment by Days 21 and 24, whereas C3, IL-15 and IL-15Ralpha were highly stained in both glandular and stromal compartments. After LCM, gene expression of DAF was 4.8-fold increased in epithelium versus stroma, whereas for OPN there was a 2-fold increase. For IL-15, the expression in stroma was 8.7-fold higher than in epithelial cells. The progressive increase of the expression of these immunomodulatory genes, proteins and ligands during the WOI, support a critical role at the time of endometrial receptiveness.