High cardiorespiratory fitness (CRF) is associated with a reduced risk of Type 2 diabetes mellitus (T2DM) and improved beta-cell function; genetic factors also determine these risks. This cross-sectional study investigated whether CRF modifies the association of polygenic risk of T2DM with glucose metabolism in nondiabetic Japanese men. Fasting plasma glucose, insulin, and glycated hemoglobin (HbA1c) levels were measured in 174 Japanese men (age: 20-79 yr). beta-Cell function and insulin resistance were evaluated by calculating HOMA-beta and HOMA-IR, respectively. CRF was assessed by measuring maximal oxygen uptake ((V) over dot(O2max)). Subjects were divided into the low and high CRF groups within each age group according to the median (V) over dot(O2max). Eleven single nucleotide polymorphisms (SNPs) associated with T2DM were analyzed and used to calculate genetic risk score (GRS); subjects were divided into the low, middle, and high GRS groups. The high GRS group had higher HbA1c levels than the low GRS group in both the low and high CRF groups (P < 0.05). Furthermore, the individuals with a high GRS had a lower HOMA-beta than those with a low GRS regardless of CRF (P < 0.05). In multiple linear regression analysis, although GRS was a significant predictor of HbA1c (beta = 0.153, P = 0.025), (V) over dot(O2max) was also associated with HbA1c (beta = -0.240, P = 0.041) independent of GRS. These results suggest that CRF is associated with HbA1c levels independent of GRS derived from T2DM-related SNPs; however, it does not modify the association of GRS with increased HbA1c or impaired beta-cell function.