Endometrial receptivity is essential for embryo implantation and ongoing successful pregnancy. The temporal "window" during which the endometrium allows implantation, known as window of implantation (WOI), which is, characterized alteration of many genes. Transcriptomic changes at the time of implantation let us discover many genes and their protein products whose altered expression effects endometrial receptivity. New omics technologies helped us to understand the complex dynamics of endometrium. Progesterone is responsible for decidualization and establishment of implantation. In women with endometriosis progesterone resistance might impair decidualization and subsequent implantation in different ways. We summarized the effects of progesterone resistance on genes, transcription factors, proteins and inflammatory mediators. Understanding the effects of progesterone resistance on genes and downstream targets will highlight future treatments in patients with endometriosis.