STUDY QUESTION: Do the determinants of insulin sensitivity/resistance differ in women with and without polycystic ovary syndrome (PCOS)? SUMMARY ANSWER: Peri-muscular thigh adipose tissue is uniquely associated with insulin sensitivity/resistance in women with PCOS, whereas adiponectin and thigh subcutaneous adipose are the main correlates of insulin sensitivity/resistance in women without PCOS. WHAT IS KNOWN ALREADY: In subject populations without PCOS, insulin sensitivity/resistance is determined by body fat distribution and circulating concentrations of hormones and pro-inflammatory mediators. Specifically, visceral (intra-abdominal) adipose tissue mass is adversely associated with insulin sensitivity, whereas thigh subcutaneous adipose appears protective against metabolic disease. Adiponectin is an insulin-sensitizing hormone produced by healthy subcutaneous adipose that may mediate the protective effect of thigh subcutaneous adipose. Testosterone, which is elevated in PCOS, may have an adverse effect on insulin sensitivity/resistance. STUDY DESIGN, SIZE, DURATION: Cross-sectional study of 30 women with PCOS and 38 women without PCOS; data were collected between 2007 and 2011. PARTICIPANTS/MATERIALS, SETTING, METHODS: Participants were group-matched for obesity, as reflected in BMI (Mean ± SD; PCOS: 31.8 ± 6.0 kg/m2; without PCOS: 31.5 ± 5.0 kg/m2). The whole-body insulin sensitivity index (WBISI) was assessed using a mixed-meal tolerance test; Homeostasis Model Assessment-Insulin resistance (HOMA-IR) was determined from fasting insulin and glucose values. Adipose tissue distribution was determined by computed tomography (CT) scan. Partial correlation analysis, adjusting for total fat mass, was used to identify correlates of WBISI and HOMA-IR within each group of women from measures of body composition, body fat distribution, reproductive-endocrine hormones and adipokines/cytokines. Stepwise multiple linear regression analysis was used to identify the variables that best predicted WBISI and HOMA-IR. MAIN RESULTS AND THE ROLE OF CHANCE: Among women with PCOS, both WBISI and HOMA-IR were best predicted by peri-muscular adipose tissue cross-sectional area. Among women without PCOS, both WBISI and HOMA-IR were best predicted by adiponectin and thigh subcutaneous adipose tissue. LIMITATIONS, REASONS FOR CAUTION: Small sample size, group matching for BMI and age, and the use of surrogate measures of insulin sensitivity/resistance. WIDER IMPLICATIONS OF THE FINDINGS: Because insulin resistance is the root cause of obesity and comorbidities in PCOS, determining its cause could lead to potential therapies. Present results suggest that peri-muscular adipose tissue may play a unique role in determining insulin sensitivity/resistance in women with PCOS. Interventions such as restriction of dietary carbohydrates that have been shown to selectively reduce fatty infiltration of skeletal muscle may decrease the risk for type 2 diabetes in women with PCOS. STUDY FUNDING/COMPETING INTERESTS: The study was supported by National Institutes of Health grants R01HD054960, R01DK67538, P30DK56336, P60DK079626, M014RR00032 and UL1RR025777. The authors have no conflicts of interest. TRIAL REGISTRATION NUMBER: NCT00726908.