Background: Visceral obesity and high body fat percentages are related to metabolic syndrome (MetS) in all ethnic groups. Based on the International Diabetes Federation (IDF) definition of MetS, the aim of the study was to explore thresholds of body fat (BF%) and the visceral fat area (VFA) for the prediction of MetS among Colombian university students. Methods: A cross-sectional study was conducted on 886 volunteers (51.9% women, mean age= 21.4 years). Weight, height, serum lipids indices, blood pressure, fasting plasma glucose, and waist circumference were measured. BF% and VFA were calculated by bioelectrical impedance analysis (BIA). MetS was defined as including ≥ 3 of the metabolic abnormalities according to the IDF definition.Results: The overall prevalence of MetS was found to be 5.9%, higher in men compared to women. BF% and VFA was positively correlated to MetS components (all p < 0.001). The optimal cutoff values for BF% in predicting MetS were 31.9% (sensitivity and specificity of 78.6 and 76.7%) in women and 20.3% in men (sensitivity and specificity of 79.5 and 82.5%). ROC curve for participants showed that VFA ≥ 4.9 mm in women and 4.3 mm in men are an indicator to best predict MetS for prediction in university students from Colombia. Conclusion: Based on the IDF criteria, both indexes were able to predict MetS in our population.