Objective: Polycystic ovary syndrome is a heterogeneous disorder characterized by oligo or anovulation, biochemical or clinical manifestations of hyperandrogenemia and polycystic ovaries. The aim of this study was to compare clinical, hormonal, and metabolic variables among polycystic ovary syndrome phenotypes. Material and Methods: This prospective cohort study was conducted in Ufuk University School of Medicine and Zekai Tahir Burak Women Health, Education and Research Hospital between October 2013 and May 2015. During this period, a total of 760 subjects were diagnosed as PCOS and were defined as eligible for the prospective follow-up. Patients with PCOS were further divided into four main phenotypes based on diagnostic features. Additionally, total of 93 subjects were included in the prospective follow-up as for the control group. Clinical and biochemical variables were compared between PCOS phenotypes and the control group. Results: The overall prevalance of phenotypes 1, 2, 3 and 4 in our population were found as 45.7%, 10%, 17.8% and 26.6%, respectively. Phenotype I was the most hyperandrogenic group in terms of clinical and biochemical features and associated with higher waist-to-hip ratio when compared with other phenotypes. Body mass index (BMI) values were significantly higher in Phenotype 1 and 2 than other phenotypes and controls. Mean systolic and diastolic blood pressure of each phenotype were significantly higher than the control group (p<0.05). Homeostatic Model Assessment Insuline Resistance (HOMA-IR) levels were significantly higher in phenotype 1 than other groups (p<0.05). Metabolic Syndrome prevalance was significantly higher in phenotype 1 when compared with other phenotypes (p<0.05). Conclusion: There are significant differences in terms of clinical, hormonal. metabolic features between different PCOS phenotypes that evaluated according to diagnostic criterias. Since each phenotype reveals different metabolic and cardiovascular risks, subjects that diagnosed with PCOS should be carefully evaluated and classified according to individual phenotype. Following appropriate phenotypical classification of patients that diagnosed with PCOS, short and long term health risks would be better clarified.