Objective Although androgen excess is necessary for the diagnosis of polycystic ovary syndrome (PCOS), insulin resistance is considered to be primarily important for the development of cardiovascular risk in PCOS. Visceral fat accumulation is more strongly related to insulin resistance than to excess total adiposity. We aimed to evaluate whether androgen excess can predict the cardiovascular risk including visceral adiposity and metabolic syndrome in young women with PCOS. Methods Between, October 2012 and January 2013, total of 317 previously A total of 1,034 women were diagnosed as PCOS by Rotterdam criteria; any two of 1) oligomenorrhea (OM), 2) biochemical or clinical hyperandrogenism (HA), and 3) polycystic ovary morphology (PCOM). We also grouped the women with PCOS into four different phenotypes; OM + HA + PCOM, OM + HA, OM + PCOM, and HA + PCOM. Visceral adiposity was defined as visceral adiposity index (VAI) ≥ 1.79, as previously reported. Results PCOS women with visceral adiposity was significantly older compared with those without visceral adiposity (25 ± 6 vs. 23 ± 4, P < 0.006). Frequencies of metabolic syndrome (36.4 vs. 1.5 %, P < 0.0001) and abnormal glucose regulation (20.9 vs. 3.8%, P < 0.0001) were significantly higher compared with those without visceral adiposity. Frequencies of visceral adiposity were significantly higher in OM + HA, OM + HA + PCO, HA + PCO, and OM + PCO (26.5, 23.8, 18.9, and 13.5%, P for trend = 0.007). Hyperandrogenism was significantly associated with visceral adiposity after adjustment for age, systolic and diastolic blood pressure, total and LDL cholesterol, fasting and postload 2-h glucose, fat mass, and menstrual cycle length (OR 2.6, 95% CI 1.7~4.1). Conclusion In conclusion, hyperandrogenemia is an important phenotype of PCOS to predict the visceral adiposity and the metabolic abnormalities.