Background and aims: Abnormalities in mitochondrial oxidative phosphorylation (OXPHOS) and insulin signaling have been implicated in the pathogenesis of skeletal muscle insulin resistance in type 2 diabetes. We hypothesized that altered expression of OXPHOS and insulin signaling genes could be of similar importance for insulin resistance in the polycystic ovary syndrome (PCOS). Materials and methods: Using the HG-U133 Plus 2.0 expression array from Affymetrix, we analyzed gene expression in skeletal muscle from obese women with PCOS (n=16) and age- and body mass index-matched control women (n=13) metabolically characterized by euglycemic-hyperinsulinemic clamp and indirect calorimetry. First, Welch's two sample t-test was applied to examine the significance of OXPHOS and insulin signaling genes separately. The overall significance of the OXPHOS and insulin signaling genes was assessed by calculating a sum statistic and conducting a permutation test. Subsequently, we performed biological pathway analysis using Gene Set Enrichment Analysis (GSEA) and Gene Microarray Pathway Profiler (GenMAPP). Results: Women with PCOS were characterized by fasting hyperinsulinemia and impaired insulin-stimulated glucose disposal - caused by reduced glucose oxidation and storage - as well as impaired suppression of lipid oxidation (all P<0.01). These abnormalities were associated with a significant decrease in the selected subset of nuclear-encoded genes involved in mitochondrial OXPHOS (P<0.03) and a significant regulation of genes involved in insulin signaling (P<0.02). GSEA and GenMAPP both revealed the same set of genes involved in OXPHOS, which was also the most downregulated biological pathway (P<0.01). Insulin signaling was significantly regulated using GenMAPP (P<0.02). These findings are currently being validated by quantitative real-time PCR and immunoblot analyses. Conclusion: Our results, for the first time, provide evidence for an association between insulin resistance and impaired mitochondrial oxidative metabolism in skeletal muscle in women with PCOS. Furthermore, differential expression of genes in the insulin signaling pathway may contribute to insulin resistance in PCOS. These abnormalities may play an important role for the increased risk of type 2 diabetes observed in these women.