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Background & Objective: Malnutrition is one of the main nutritional problems among children under 5 years especially in developing countries. The effects of malnutrition in this range of age group includes ; disorder of mental and physical growth and development, increase in the morbidity and mortality, decrease of the learning capacity. A detailed epidemiological picture of the prevalent malnutrition status among children under 5 years in different regions of Iran enables health policy makers to identify priorities, establish political commitment and design appropriate interventional programs to prevent and control malnutrition and improve nutritional status of children. To determine the prevalence rate of malnutrition among children under 5 years. Methods: Demographic data, weight and height of 34200 Iranian children between 0-72 months old in 28 provinces of the country in 2005 year based on a cluster sampling were gathered. The subjects' weight and height were measured by trained staff. Prevalence of underweight, stunting, and wasting indicators was determined by measuring the weight and height of subjects in urban and rural areas. EPI6 statistical software, version b6/04, was used for all statistical analyses. Results: 4.7% of the children aged less than five years suffered from stunting (95% CI: 4.5- 4.9%) The prevalence of this type of malnutrition among urban children is significantly less than rural children (95% CI: 3.1- 3.5% and 6.5-7.1% respectively). Meanwhile the prevalence of underweight was 5.2% in the country (95% CI: 5.1-5.4% while the prevalence of this type of malnutrition was significantly less among urban children than those in rural ones. Moreover, the prevalence of wasting was 3.7% (95%CI: 3.5-3.9%) and there was a significant difference in this regard between the urban and rural children. Thus this indicator was significantly higher among urban children than those in rural areas (95%CI: 3.8-4.3% and 3.0-3.5% respectively). Conclusion: The results of the study show that the prevalence of protein-energy malnutrition was low among Iranian children under five years old. In comparison with previous studies, it is felt that there has been a prudent decrease in all malnutrition in all levels. However, there were significant differences in the prevalence of malnutrition in different provinces, which has resulted in the differences in their developmental stages as well. It appears that subjective strategies are required to improve the nutritional and health status among children under five in all provinces.