Physically fit individuals have a lower risk of cardiovascular disease and type 2 diabetes. However, it is unknown whether the associations between physical fitness and the metabolic syndrome are independent of total and abdominal adiposity. Physical fitness was defined as the physical work capacity on a cycle ergometer at heart rate of 150 bpm (PWC 150) in a sample of 158 men and 198 women 20-60 years of age. PWC 150 was adjusted for fat-free mass prior to the analyses. Percent body fat was estimated by hydrostatic weighing. Visceral and subcutaneous abdominal fat were measured by computed tomography. The prevalence of the metabolic syndrome was based on two definitions. The metabolic syndrome decreased with increasing fitness in men (approx. 6 times higher in less fit vs. most fit tertile, p < 0.05) and in women (approx. 4 times higher in less fit vs. most fit tertile, p < 0.05). Fitness was negatively associated with most individual components of the metabolic syndrome, except HDL-cholesterol for which the correlation was positive. However, in men and in women, the effects of physical fitness on the individual components of the metabolic syndrome were attenuated after considering total and abdominal adiposity.