Childhood obesity is a medical and social problem in Japan. The number of obese children has been increasing steadily since 1980 according to a survey on school health statistics. However, more simple and reliable criteria for assessment of obesity in children are required. The aim of this study was to establish gender- and age-specific body mass index (BMI) cutoff values for evaluation of obesity in school-aged children. A total of 100,587 elementary school, junior and senior high school students, aged 6 to 17 years, comprised the study population, in whom BMI was measured. The BMI cutoff values were calculated by using the receiver operating characteristic (ROC) analysis in the degree of obesity of 20% or greater as definition of obesity. The validity of the determined cutoff values of BMI was then compared with the Rohrer index, the International Obesity Task Force (IOTF) data and the percentile method. The sensitivity and specificity of the BMI cutoff values were over 93% in both boys and girls of all ages, thereby providing criteria that are highly diagnostic in all ages. The Rohrer Index and BMI 95th percentile values tended to underestimate obesity, while the IOTF criteria tended to overestimate it. In conclusion, the BMI cutoff values determined in the present study enable us to detect obese individuals with extremely high precision, and thus may represent an instrument with superior diagnostic capabilities to those of the existing instruments currently being used for assessment of pediatric obesity.