Objectives: The purpose of this review is to provide an overview of existing studies on the specificities of gene expression in the endometrium in PCOS and possible molecular mechanisms linking those specificities with reproductive and obstetric consequences of PCOS. Mechanism: Polycystic ovary syndrome (PCOS) is a complex disorder combining features of reproductive, metabolic, and psychological disturbances. The effect of metabolic, inflammatory, and endocrine abnormalities on ovulatory function and oocyte quality has been seen as the main reproductive issue in PCOS women. However, even after the restoration of ovulation, this group exhibits lower than expected reproductive outcomes. Functionally relevant sequence alterations in genes involved in regulating endometrial receptivity could also be relevant in PCOS as a property independent of extra-endometrial influences. Findings: Hyperandrogenism, ovulatory dysfunction, and insulin resistance are associated with the alterations in endometrial gene expressions leading to suboptimal endometrial receptivity in PCOS. Endometrial steroid receptor malfunction seems to be a contibuting factor to the intrinsic suboptimal endometrial receptivity in PCOS. Conclusion: epigenetic or epigenomics mechanisms altering gene expressions on the endometrial level in PCOS should not be ruled out. Future studies should focus on investigating specificities of each PCOS phenotype and developing individual treatment strategies to meet the specific needs of every PCOS patient.