A necessary condition for establishing new criteria for the metabolic syndrome (MetS) in Japan is waist circumference (WC), which varies among races. In the present study, we measured WC and visceral fat area (VFA) in patients with chronic kidney disease (CKD) and assessed the features of new MetS criteria in Japan. Two hundred and seventeen patients (M/F: 116/101, age: 59.1 ± 13.0 years, body mass index: 24.1 ± 3.9 kg/m2) who received abdominal computed tomography (CT) examinations were analyzed, and 93 subjects met the criteria for MetS. Average VFA was significantly larger in subjects with MetS (193.6 ± 52.4 cm2 versus 96.9 ± 50.2 cm2, P < 0.001). WC and VFA correlated significantly in both males (r = 0.71, P < 0.001) and females (r = 0.79, P < 0.001). Male and female CKD patients whose VFAs exceed 125 cm2 have significantly more components of MetS, and the corresponding WC is 81.2 cm for males and 81.6 cm for females. From the ROC curve, 84 cm for males and 83 cm for females seemed to be suitable cut-off values in CKD patients. In conclusion, we propose suitable cut-off values of WC in Japanese CKD patients, with a high sensitivity for detecting the MetS, to be 84 cm for males and 83 cm for females. Further prospective analysis is required to validate these criteria and the clinical significance of MetS in Japanese CKD patients.