Polycystic Ovary Syndrome (PCOS) is the most common endocrinopathy among reproductive age women which is a major cause of reproductive and metabolic irregularities. The features of PCOS are oligo/anovulation, hyperandrogenism, polycystic ovaries. These features are associated with hirsutism, acne, infertility, insulin resistance, obesity and inflammation. Commonly, adipose tissue of women with PCOS display abnormalities which are linked to inflammation and insulin resistance that are central factors in PCOS. This study focused on the aberrant mechanisms in adipocytes that are related to PCOS etiology. For this purpose, gene expression in adipose tissue of women with PCOS was analysed and compared to healthy controls. The statistical analysis of an Illumina microarray data set yielded a list of significantly differentially expressed genes, and gene set enrichment analysis revealed that the upregulated genes (PTPN6, HLA-DRB1 and MYD88) are involved in pathways that are related to immunity, and the downregulated genes (such as PER2) contribute to circadian rhythm. Expression of these genes were verified in adipose tissue of PCOS-like mouse models, using quantitative Real-Time Polymerase Chain Reaction (qPCR). However, the results of gene expression verification do not lie in accordance with what is expected, since no differences in expression of the selected genes in adipose tissue of PCOS-like mouse models were observed. In conclusion, only adipose tissue of women with PCOS showed differences in the expression of key genes which have pathologic role in PCOS. These genes play critical role in systemic inflammation, insulin resistance and hyperandrogenism.