Establishment of early pregnancy is promoted by a complex network of signalling molecules that mediate cell-to-cell and cell-to-extracellular matrix communications, in order to manifest controlled invasion of the trophectoderm and successful implantation. During the period known as the 'window of implantation', the endometrium expresses specialized proteins, many of which exhibit potential use as markers of endometrial receptivity. Trophoblast differentiation to the invasive phenotype also depends on the up-regulation of certain peptides and the down-regulation of others. Disruption of each pathway is theoretically possible, and studies in animal models suggest that implantation defects result when the function of these proteins is blocked. Indeed, the implantation process is currently considered the most important limiting factor for the establishment of viable pregnancy. The present overview of the literature reports critical families of molecules located at the embryo-maternal interface and describes the mechanisms of interplay and control. Since these factors are crucial to the process of implantation, targeting them might be a valuable contraceptive tool. Conversely, induction of specific peptides may prove to be beneficial in certain infertility cases.