Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects women in their reproductive age. It is characterized by hyperandrogenism, menstrual cycle irregularities and polycystic ovarian morphology. PCOS can cause infertility and is usually associated with a number of metabolic dysfunctions such as insulin resistance and aberrant fat metabolism in major metabolic organs such as skeletal muscles. These dysfunctions increase the risk for developing diabetes and cardiovascular diseases. The exact etiology of PCOS is still unknow, but a number of genetic, epigenetic and environmental factors have been identified. In order to understand the links between PCOS and its related metabolic dysfunction, and to unravel its complex pathophysiology, extensive research is constantly done. In this study, 84 differentially expressed genes have been identified in skeletal muscles of women with PCOS (n=13) compared to controls (n=12) by array-based RNA profiling. Using gene set enrichment analysis, it is demonstrated that these genes are components of metabolic pathways that are related to fat metabolism and transport. In vitro verification of differential gene expression of 5 genes of interest in skeletal muscles from prenatally androgenized mice was done using RT-PCR, and shows statistically significant differential expression of 2 out of 5 genes. This study confirms the role of fat metabolism in PCOS pathogenesis and uses knowledge learned from obesity and diabetes to suggest directions for further research, which is warranted to develop new treatments that will; hopefully, reduce the devastating effects of PCOS on the lives of women and the economies of communities worldwide.