STUDY QUESTION: Do women with the polycystic ovary syndrome (PCOS) differ from those with the metabolic syndrome (MetS) in markers of insulin resistance (IR) and circulating androgens?SUMMARY ANSWER: Women with MetS have more pronounced IR than those with PCOS whereas only the latter have elevated circulating androgens.WHAT IS KNOWN ALREADY: PCOS and MetS share many similarities, including abdominal obesity and IR, and PCOS is regarded as the ovarian manifestation of MetS. However, there are limited data on the differences between markers of IR and circulating androgens between women with these two syndromes.STUDY DESIGN, SIZE, DURATION: A prospective study in 1223 Caucasian women with PCOS and 277 women without PCOS, matched for BMI, was performed between May 2004 and December 2011. The presence/absence of MetS in PCOS+ and PCOS- women was recorded and comparisons among the resulting four groups were performed.PARTICIPANTS/MATERIALS, SETTING, METHODS: This study was performed in a university department of obstetrics and gynecology. The following markers of IR were determined: serum glucose and insulin levels, glucose/insulin ratio, area under the oral glucose tolerance test, homeostasis model assessment of IR index and quantitative insulin sensitivity check index.MAIN RESULTS AND THE ROLE OF CHANCE: PCOS+MetS+ women (n = 361) were more insulin-resistant than PCOS+MetS- women (n = 862) (P < 0.001 for the comparisons in all markers of IR). Similarly, PCOS-MetS+ women (n = 66) were more insulin-resistant than PCOS-MetS- women (n = 211) (P < 0.001 for the comparisons in all markers of IR). In contrast, PCOS+MetS+ showed only borderline significant differences in some markers of IR compared with PCOS-MetS+ women (P < 0.05). Similarly, PCOS+MetS- women showed only borderline significant differences in some markers of IR compared with PCOS-MetS- women (P = 0.037). Moreover, PCOS-MetS+ women were more insulin-resistant than PCOS + MetS- women (P < 0.001 for the comparisons in all markers of IR). Regarding circulating androgens, PCOS+MetS+ women had higher levels of circulating androgens than PCOS-MetS+ women (P < 0.001 for the comparisons in all circulating androgens). Similarly, PCOS+MetS- women had higher levels of circulating androgens than PCOS-MetS- women (P < 0.001 for the comparisons in all circulating androgens). In contrast, circulating androgens did not differ between PCOS+MetS+ women and PCOS+MetS- women. Similarly, circulating androgens did not differ between PCOS-MetS+ women and PCOS-MetS- women.LIMITATIONS, REASONS FOR CAUTION: Only Caucasian women were included in the study. IR was not assessed with the euglycemic hyperinsulinemic clamp.WIDER IMPLICATIONS OF THE FINDINGS: Even though MetS and PCOS have many similarities, they are distinct disorders. PCOS does not appear to simply represent the ovarian manifestation of MetS. Further studies are required to assess the contribution of hyperandrogenism to the pathogenesis of IR in PCOS.STUDY FUNDING/COMPETING INTEREST(S): No external funding was either sought or obtained for this study.