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Background Cardiorespiratory fitness (CRF) has been inversely associated with insulin resistance and clustering of cardiometabolic risk factors among overweight and obese individuals. However, most previous studies have scaled CRF by body mass (BM) possibly inflating the association between CRF and cardiometabolic health. We investigated the associations of peak oxygen uptake (V O2peak) and peak power output (Wpeak) scaled either by BM-1, fat free mass (FFM-1), or by allometric methods with individual cardiometabolic risk factors and clustering of cardiometabolic risk factors in 55 overweight or obese adults with metabolic syndrome. Methods V O2peak and Wpeak were assessed by a maximal cycle ergometer exercise test. FFM was measured by air displacement plethysmograph and glucose, insulin, HbA1c, triglycerides, and total, LDL, and HDL cholesterol from fasting blood samples. HOMA-IR and metabolic syndrome score (MetS) were computed. Results V O2peak and Wpeak scaled by BM-1 were inversely associated with insulin (β=-0.404 to -0.372, 95% CI=-0.704 to -0.048), HOMA-IR (β=-0.442 to -0.440, 95% CI=-0.762 to -0.117), and MetS (β=-0.474 to -0.463, 95% CI's=-0.798 to -0.127). Other measures of CRF were not associated with cardiometabolic risk factors. Conclusions Our results suggest that using BM-1 as a scaling factor confounds the associations between CRF and cardiometabolic risk in overweight/obese adults with the metabolic syndrome.