The aim of this study was to analyze body fat anthropometric equations and electrical bioimpedance analysis (BIA) in the prediction of cardiovascular risk factors in eutrophic and overweight adolescents. 210 adolescents were divided into eutrophic group (G1) and overweight group (G2). The percentage of body fat (% BF) was estimated using 10 body fat anthropometric equations and 2 BIA. We measured lipid profiles, uric acid, insulin, fasting glucose, homeostasis model assessment-insulin resistance (HOMA-IR), and blood pressure. We found that 76.7% of the adolescents exhibited inadequacy of at least one biochemical parameter or clinical cardiovascular risk. Higher values of triglycerides (TG) (P = 0.001), insulin, and HOMA-IR (P < 0.001) were observed in the G2 adolescents. In multivariate linear regression analysis, the % BF from equation (5) was associated with TG, diastolic blood pressure, and insulin in G1. Among the G2 adolescents, the % BF estimated by (5) and (9) was associated with LDL, TG, insulin, and the HOMA-IR. Body fat anthropometric equations were associated with cardiovascular risk factors and should be used to assess the nutritional status of adolescents. In this study, equation (5) was associated with a higher number of cardiovascular risk factors independent of the nutritional status of adolescents.