The endometrium undergoes cyclic changes in response to circulating ovarian steroid hormones as it prepares for implantation. This dynamic tissue is well suited to microarray expression profiling for elucidation of molecular players participating in the maturation of the endometrium and during the process of implantation. Recent advances in sequencing the human and mouse genomes and the availability of microarray technology and bioinformatic analyses have made elucidating these molecular participants and dialogs a reality. Analysis of the window of implantation, a temporal and spatially unique period in which the endometrium is receptive to embryonic implantation, has revealed numerous processes to be occurring simultaneously or sequentially. These include cell cycle regulation, angiogenesis, immune modulation of implantation, defense mechanisms put into place by antibacterial agents and detoxicants, secretion of unique products, transport of ions and water, growth factor actions, steroid hormone action and metabolism, and production of extracellular matrix proteins, unique cell surface glycoproteins, and a variety of transcription factors, to name a few. Several groups have recently conducted studies with human endometrium, and remarkable similarities exist with mouse. Also, many genes and gene families involved in the unique differentiation process of stromal cell decidualization are conserved. In addition, infertility associated with endometriosis is partly implantation-based, and gene profiling of such tissue during the window of implantation has revealed additional insight into mechanisms underlying infertility in this disorder. Global profiling of genes in the endometrium, decidua, and at the interface between the trophoblast and the decidua, has provided remarkable in sight into endometrial maturation and implantation.