The objective of the present study was to evaluate the predictive values of percent body fat (PBF) and body mass index (BMI) for cardiovascular risk factors, especially when PBF and BMI are conflicting. BMI was calculated by the standard formula and PBF was determined by bioelectrical impedance analysis. A total of 3859 ambulatory adult Han Chinese subjects (2173 males and 1686 females, age range: 18-85 years) without a history of cardiovascular diseases were recruited from February to September 2009. Based on BMI and PBF, they were classified into group 1 (normal BMI and PBF, N = 1961), group 2 (normal BMI, but abnormal PBF, N = 381), group 3 (abnormal BMI, but normal PBF, N = 681), and group 4 (abnormal BMI and PBF, N = 836). When age, gender, lifestyle, and family history of obesity were adjusted, PBF, but not BMI, was correlated with blood glucose and lipid levels. The odds ratio (OR) and 95% confidence interval (CI) for cardiovascular risk factors in groups 2 and 4 were 1.88 (1.45-2.45) and 2.06 (1.26-3.35) times those in group 1, respectively, but remained unchanged in group 3 (OR = 1.32, 95%CI = 0.92-1.89). Logistic regression models also demonstrated that PBF, rather than BMI, was independently associated with cardiovascular risk factors. In conclusion, PBF, and not BMI, is independently associated with cardiovascular risk factors, indicating that PBF is a better predictor.