Clinical observations indicate that an implantation defect occurs in women with endometriosis. Despite intense research, the role of alterations in endometrial receptivity and the peritoneal fluid microenvironment in the derangement of implantation in endometriosis remains controversial. In this review, the evidence for the altered endometrial receptivity and peritoneal environment are summarized, and their effects on the implantation defect in women with endometriosis are discussed. Recent studies on cell adhesion molecules and their ligands, apoptosis, homeobox genes and the direct action of gonadotrophin-releasing hormone analogues are reviewed with respect to their contribution to endometrial receptivity in endometriosis. The possible mechanisms by which an altered peritoneal environment of endometriosis may affect implantation, including cytokine concentrations, iron metabolism, biochemical factors and embryotoxicity are discussed.