Objectives To investigate the prevalence of non-alcoholic fatty liver disease (NAFLD) in children and its relationship to metabolic syndrome, insulin resistance, and waist circumference (WC). Methods This was a population-based cross-sectional, case-control study. Cases were selected among students of a primary and junior high school, respectively, and ageand sex-matched control subjects were selected randomly (ratio of cases to control subject was 37:113). Results Of the 846 students, aged between 6 and 15 years, enrolled in the study and screened by ultrasonography, 37 children were diagnosed as having NAFLD (score C 1). There was a significant sex difference in the prevalence of NAFLD(P = 0.003). The trend test revealed a strong doseresponse relationship (P \ 0.001) between pediatric NA-FLD and the number of the proposed components of pediatric metabolic syndrome in Japan (MetS-JC), such as a clustering of the components of MetS-JC. Additionally, the linear trend of the odds ratios (ORs) with increasing percentile of the homeostasis model assessmentinsulin resistance (HOMA-IR) was statistically significant (P \ 0.001). However, when WC was added to the logistic model, the ORs were no longer significant, whereas WC turned out to be an independent risk factor for NAFLD regardless of the HOMA-IR index. Conclusion The prevalence of NAFLD in children and adolescents is closely related to metabolic syndrome, insulin resistance, and WC.