Patients with polycystic ovary syndrome (PCOS) have lower pregnancy and higher miscarriage rates, possibly due to decreased endometrial receptivity. In this study, endometrium was processed for RNA extraction and hybridization of chemically fragmented, biotinylated, complementary RNA on high-density oligonucleotide microarrays, and screened for 21,571 genes. Real-time polymerase chain reaction (PCR) was used to verify the result. Genes found to be down-regulated in the endometrium during the implantation window in PCOS patients included those whose activity was integral to membrane function, adhesion, invasive growth and the cytoskeleton. Among these genes, some have previously been associated with endometrial receptivity (by microarray research or other methods) and some have never previously been associated with endometrial receptivity. Using real-time PCR, expression of transmembrane 4 superfamily member 4 (TM4SF4) and matrix metalloproteinase 26 (MMP26) was found to be significantly decreased during the implantation window in patients with PCOS (P= 0.003). TM4SF4 has been demonstrated to be associated with adhesion; MMP26 has been shown to be related to degradation of extracellular matrix. It is suggested the down-regulated gene expression during the implantation window in patients with PCOS indicates differential gene expression in the endometrium between PCOS and normal women during the implantation window. This might affect endometrial receptivity.