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Objective We investigated the relationship of the waist circumference (WC) and body fat weight (BF) with insulin resistance in subjects with normal body mass index (BMI) and normal glucose tolerance (NGT) during a routine medical check-up. Methods We categorized 167 male subjects in three groups as follows: a group with normal BMI but high WC (normal-BMI/high-WC group; 22≤BMI<25 kg/m(2), waist ≥85 cm; n=31), a group with normal BMI and normal WC (normal-BMI/normal-WC group, waist <85 cm; n=68), and a group with low normal BMI and normal WC (low normal-BMI/normal-WC group; 18.5≤BMI<22 kg/m(2) and waist<85 cm; n=68). We measured the plasma glucose and serum insulin levels before glucose loading and after 30 and 120 minutes and calculated several indexes of insulin secretion and sensitivity. Results Subjects from the normal-BMI/high-WC group showed significantly decreased Matsuda index and increased homeostasis model assessment for insulin resistance (HOMA-IR) compared with normal-BMI/normal-WC group. Univariate regression analyses showed significant correlation of HOMA-IR with WC (r=0.39) and BF (r=0.37). Matsuda index was significantly correlated with WC (r=-0.39) and BF (r=-0.47). The multiple regression analysis showed that the BF is significantly correlated with HOMA-IR (p<0.05) and Masuda index (p<0.005) among the clinical variables and with HOMA-IR (p<0.05) and Masuda index (p<0.0001) among the anthropometric variables but not with WC in either analysis. Conclusion Decreased Matsuda index and increased HOMA-IR were observed in subjects from the normal-BMI/high-WC group. Multivariate analysis showed that BF is associated with decreased Matsuda index and increased HOMA-IR and that WC is not associated with either factors.