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Introduction: Malnutrition remains the most serious children health problem and the most main cause of children mortality in the World Health Organization (WHO) Eastern Mediterranean Region. Nearly one-third of children in the region are either underweight or stunted, and more than 30% of the population suffers from micro-nutrient deficiencies.The aim of this study is to determine the prevalence of malnutrition among school children in Kerman. Material and Methods: This is a cross–sectional study. The number of 1,056 students recurred in Kerman, in the age range of 7 to12 years were selected by multistage sampling. Children weight for age (W / A), height for age (H / A) and weight for height (W / H) indicators was calculated and were compared with NCHS standard index. Students' height and weight were measured with standard tools. Epi-info and Stata 11 software were used for analysis. Descriptive and chi 2 tests were used to provide a comparison according to (in) gender (sex). Results: Prevalence of Malnutrition based on weight-for-age, height-for-age and weight-for-height respectively are 6.06, 5.58 and 75.9 percent and the prevalence average of malnutrition with above indicators respectively are 24.43, 26.04 and 24.90 percent. Comparison of weight-for-age and weight-for-height indices in children showed higher prevalence of malnutrition in girls than boys (P-value<0.05). Conclusion: According to results, prevalence of malnutrition among school children was high in Kerman and must identify the factors creating it, and the necessary planning should be done to eliminate them.