BackgroundThe World Health Organization (WHO-2007) and the International Obesity Task Force (IOTF-Cole) systems assess child weight status. However, derived estimations often differ. We aimed to a) compare the prevalence of overweight and obesity, b) analyze individual and contextual factors associated with child weight using multilevel analysis and c) explore the spatial distribution of overweight and obesity using both classification systems.MethodsWe used data from the 2015/2016 National School Height and Weight Census in El Salvador. Information on 111,991 children aged 6.0–9.9 years attending the first grade was analyzed. Body mass index Z-score (BMIZ), overweight and obesity were defined with both classification systems. Weighted kappa was used to measure agreement. Child, school and municipal potential determinants of BMIZ were examined by multilevel analysis. Municipal spatial clustering of overweight and obesity was tested using Moran’s Index and Getis-ord Gi* statistics.ResultsThe combined prevalence of overweight and obesity was higher according to the WHO system than the IOTF (30.4% vs 23.1%). The weighted kappa was 0.83. Boys, children attending urban schools, children attending private schools, and children residing in municipalities with high human development index had higher BMIZ than their counterparts. The Moran’s indexes were positives and significant. Clusters of high prevalence (above the national prevalence) of overweight and obesity were found in 29 municipalities using the WHO and IOTF systems. For obesity, 28 and 23 municipalities in clusters of high prevalence were detected using the WHO and IOTF criteria, respectively.ConclusionsOverweight and obesity is high among school-age children in El Salvador. The prevalence of overweight and obesity was higher when using the WHO system, as compared to the IOTF system. Irrespective of the classification system, the multilevel and spatial analysis derived similar interpretations. These results support the need for national preventive interventions with targeting strategies to reduce overweight and obesity in school-age children.