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Introduction: polycystic ovary syndrome (PCOS) is associated with cardiovascular disease (CVD) risk factors. First-line therapy for PCOS is lifestyle changes including exercise. We compared CVD risk factors between women with and without PCOS and examined the responses to high-intensity interval training (HIIT). Methods: women with PCOS were randomized to HIIT (n = 41) or a non-exercise control group (n = 23) for 16 weeks. Women without PCOS (n = 15) were age- and BMI-matched to participants with PCOS and completed 16 weeks of HIIT. CVD markers included blood pressure, heart rate, flow mediated dilatation (FMD), carotid intima-media thickness (IMT), and circulating concentrations of lipids, glucose, insulin, and matrix metalloproteinase-9 (MMP-9). Results: resting heart rate was higher in women with PCOS than without PCOS (p =0.011) and was reduced after HIIT in women with PCOS (−2.8 beats/min, 95% CI: −5.4, −0.2, p = 0.037). FMD was not significantly different between women with PCOS (5.5%, SD 4.1) and those without PCOS (8.2%, SD 3.9) at baseline. HIIT reduced time-to-peak dilatation of the brachial artery in women with PCOS compared with women without PCOS (−55 s, 95% CI: −96, −13, p = 0.012). Conclusions: we found little difference in CVD risk factors between women with and without PCOS at baseline, but some indications of endothelial dysfunction in women with PCOS.