Type 2 diabetes is increasing globally and in Asia. The purpose of this study was to examine the association of a fit-fat index (FFI) with diabetes incidence among Japanese men. In total 5,014 men aged 18-64 years old, who had an annual health check up with no history of major chronic disease at baseline from 2002 to 2009 were observed. CRF was estimated via cycle ergometry. Overall, 7.6% of the men developed diabetes. The mean follow-up period was 5.3 years. Hazard ratios, 95% confidence intervals and P trend for diabetes incidence were obtained using the Cox proportional hazards model while adjusting for confounding variables. High FFI demonstrated lower risk 0.54 (0.36-0.82) compared to low BMI 0.63 (0.44-0.90), low WHtR 0.64 (0.41-1.02), and High CRF 0.72 (0.51-1.03). FFI showed a marginally stronger dose response relationship across quartiles (P (trend) =0.001) compared to BMI (P (trend) =0.002), WHtR (P (trend) =0.055), and CRF (P (trend) =0.005). Overall, both fitness and fatness play independent roles in determining diabetes incidence in Japanese men. FFI may be a more advantageous physical fitness measure because it can account for changes in fitness and/or fatness.