New biological markers are emerging trying to identify earlier cardiovascular high risk subjects. Myeloperoxidases have been involved in the role of atherosclerosis process, by the beginning of the endothelial dysfunction up to the plaque rupture and clinical manifestation, and it has been demonstrated that this enzyme has also a prognostic value. We aimed to assess myeloperoxidases levels in patients with polycystic ovary syndrome (PCOS) with insulin resistance (IR), considering that these women represent a high risk group for cardiovascular disease. We developed a transversal study, comprising 26 patients with PCOS and IR and 30 controls (PCOS without IR). IR was considered with HOMA-IR ≥3.0. IR absence was considered when HOMA-IR <3.0, triglycerides <200, BMI <28.7, and BMI<27.8 in patients with familial history of type 2 diabetes. All patients went through anamnesis, physical examination, transvaginal ultrasound, and blood samples. IR PCOS patients had higher levels of myeloperoxidase (22.3 × 18.1, p = 0.047), and also higher BMI. Myeloperoxidase levels correlated directly with insulin. In conclusion, IR PCOS young patients have higher myeloperoxidase levels.