The aim of this article was to evaluate the clinical, endocrine, and cardiovascular disease risk profile differences among main polycystic ovary syndrome (PCOS) phenotypes. One hundred and thirty-nine consecutive women were included in the study. Body mass index (BMI), serum follicle stimulating hormone (FSH), luteinizing hormone (LH), progesterone, estradiol, testosterone, dehydroepiandrosterone sulfate, fasting glucose, low density lipoprotein (LDL-C), total cholesterol, high density lipoprotein (HDL-C) high sensitive CRP, c-peptide, insulin, insulin sensitivity and carotid intima thickness were compared among different phenotype groups of PCOS: Group 1-PCO (polycystic ovaries)-anovulation (n = 34), Group 2-Hyperandrogenemia (HA)-anovulation (n = 30), Group 3-HA-PCO (n = 32), and Group 4-HA-PCO-anovulation (n = 43). Statistically significant differences among the different phenotype groups in terms of waist hip ratio, total cholesterol, LH, estradiol, fasting glucose, progesterone, free testosterone, and carotid intima media thickness were observed. The lowest mean CIMT was observed in Group 3, and the highest fasting glucose levels were in Group 4, while the lowest mean free testesterone was measured in Group 1. BMI, LDL-C, and total cholesterol showed significant positive correlations with CIMT (r = 0.411, P = 0.001; r = 0.258, P = 0.006; r = 0.199, P = 0.033). The lowest LDL-C, total cholesterol, and BMI were found in Group 3, but differences were not statistically significant. High-sensitive CRP levels were similar among the groups (P = 0.103). Group 3 PCOS with PCO and hyperandrogenemia phenotype has lower cardiovascular disease risk compared to other phenotypes.