Introduction: Child malnutrition continues to be a major public health problem in developing countries. This study aims to determine the current nutritional status of Malaysian school children using the anthropometric indicators of weight for age (WAZ), height for age (HAZ), and body mass index for age (BAZ). Methods: A nationwide school-based survey was undertaken in all Malaysian states and territories, which included 18,078 children aged 8-10 years attending 445 primary schools. The software WHO AnthroPlus was used to calculate zscores for the nutritional status (WAZ, HAZ and BAZ) of the target population relative to the World Health Organization (WHO) 2007 reference. Results: The national prevalence of underweight among school children was 13.6% and in rural areas, this rate was nearly double that of urban areas. The national prevalence rate for stunting was 10.9%, double among rural school children compared to their urban counterparts. As for thinness, the national prevalence was 6.5%. Using the WAZ indicator, we found that the national prevalence of overweight children was 7.6%. Additionally, we found that urban areas showed a higher prevalence of overweight children (8.8%) than rural areas (5.9%). Conclusion: The findings of this study indicate that Malaysian school children face the burden of malnutrition, suffering from both undernourishment and overweight. Malaysia must make a concerted effort to overcome the problems of malnutrition among children.