Objective: We aim to study the relationship between atherosclerosis and serum sclerostin levels in different phenotypes of polycystic ovary syndrome (PCOS). Materials and Methods: A total of 134 women with PCOS and 33 age-matched controls participated in this study. Women with PCOS were further divided into subgroups based on their PCOS phenotypes: phenotype A (n=35), phenotype B (n=33), phenotype C (n=31), and phenotype D (n=35). Metabolic parameters, hormonal parameters, carotid intima-media thickness (CIMT), and sclerostin levels were compared among the PCOS phenotypes. Results: Statistically significant differences occurred among groups regarding follicle-stimulating hormone, luteinizing hormone, estradiol, total cholesterol, low-density lipoprotein, Ferriman-Gallwey score, total testosterone, and free androgen index. The mean CIMT was statistically higher in all PCOS phenotypes than in controls. In subgroup comparison, phenotypes A and B had a higher body mass index (BMI) adjusted CIMT than other phenotypes, respectively (p=0.005). Serum sclerostin levels were higher in PCOS patients than in controls. A concentration of ≥6.297 ng/mL showed a sensitivity of 56% and a specificity of 69.7% to predict PCOS. The BMI-adjusted sclerostin level was significantly higher in phenotype C (20.3±0.7 ng/mL) than in other phenotypes. Conclusion: Patients with phenotypes A and B seem to have an increased risk for atherosclerosis. Although sclerostin was higher in PCOS patients, we could not demonstrate the relation between sclerostin and atherosclerosis in different PCOS phenotypes.