Background: Although both obesity, measured by body mass index, and visceral obesity are known to be major risk factors of metabolic syndrome and its components, there have been debates on the relative contribution of general obesity and visceral obesity to the development of metabolic syndrome. Methods: We performed a large longitudinal cohort study of 3,093 subjects (age range, 18–65 years) who were metabolically healthy and had a normal weight who received health screenings over a 3-year follow-up period. Cox proportional hazards models were used to estimate the adjusted hazard ratios (HRs) and 95% confidence intervals (CI) for incident metabolic syndrome and its components per sex-specific 1-standard deviation (SD) increase in visceral adipose tissue (VAT) and body mass index. Results: Both obesity and visceral obesity increased the risk of incident metabolic syndrome, but when HR was compared per sex-specific 1-SD, visceral obesity appeared to confer more risk than simple obesity. The HR for 1-SD of body mass index was 1.19 (95% CI, 1.07–1.32; P=0.001) in men and 1.29 (95% CI, 1.10–1.52; P=0.002) in women, while the HR for 1-SD of VAT was 1.29 (95% CI, 1.15–1.44; P<0.001) in men and 1.50 (95% CI, 1.28–1.75; P<0.001) in women. Conclusion Visceral obesity and obesity were longitudinally associated with an increased risk of incident metabolic syndrome among metabolically healthy adults, and visceral fat accumulation appears to be better predictor of metabolic syndrome.