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Diagnostic criteria for the metabolic syndrome (Mets) in Japan have been set by the Medical Committee of the Japanese Association of Medical Sciences (Med), the National Health and Nutrition Examination Survey (Nat), specific health checkups (Ckup), and second medical examination by Worker's Accident Compensation Insurance System (Wor). The purpose of this study was to compare classification of the metabolic syndrome by different organizational criteria and to investigate underlying differences.All faculty members of a university in Osaka, Japan, underwent mandatory health checkups in September 2008. The demographic distribution included 769 males (mean age, 49 +/- 12 years) and 415 females (mean age, 43 +/- 10 years). Using the Med, Nat, Ckup and Wor criteria, individuals were assessed for the MetS and pre-metabolic syndrome (pre-Mets), strongly suspected metabolic syndrome (S-Mets) and assumed pre-metabolic syndrome (A-pre-Mets), as well as a positive support level (PSL) and a motivational support level (MSL). All faculty members were categorized into a morbid group (Mets, S-Mets, PSL, and FB) or a pre-morbid group (pre-Mets, A-pre-Mets, and MSL) based on medical data and smoking habits. The incidence of morbid and pre-morbid individuals was compared across the four criteria and analyzed based on gender and age (under 40 and 40 or over).Male incidences for the morbid and pre-morbid classifications were 17% and 20% with Med, 9% and 23% with Nat, 27% and 14% with Ckup, and 1.4% and 0% with Wor. There were significant differences across criteria sets in both the morbid and pre-morbid groups, with significantly greater numbers of males than females, and higher prevalences in those aged 40 or over than in their younger counterparts. Males aged under 40 classified into the pre-morbid group comprised 18% in Med, 16% in Nat, and 13% in Ckup.The different disease incidences found between Med and Ckup data in males aged 40 or over might be attributed to varying criteria for blood glucose levels, while Wor data may be influenced by the higher level of blood pressure set as a criterion with this approach. It will be important to continuously validate currently established criteria to identify the actual prevalence of MetS in Japan. Furthermore, incorporation of waist circumference and BMI for females, and a positive approach for young males, may be critical for future developments.