Background: Malnutrition is steel a major health problem in the developing countries. It is recognized that 60% of death among children fewer than five years in these countries are associated with malnutrition. The aim of this study was to estimate the prevalence of malnutrition in children under 5 years old in Iranshahr in 2011. Materials and Methods: This is a cross-sectional descriptive study. The sample consisted of 700 children less than 5 years old were randomly selected by cluster and quota method among health centers. Child growth was mensured based on NCHS-WHO charts. A questionnaire was used for data collection. Data were analysed by SPSS Ver.18, using chi-square, and logistic Regression tests for comparing groups. Results: Prevalence of stunting (height for age) was 11.1%, (disorder of growth = 7.7%, severe malnutrition = 3.4%), underweight (weight for age) was 9.8% (disorder of growth = 7%). Malnutrition has significant association with birth grade, delivery type, hospitalization history, educational level of parents, parents' job, birth weight, vaccination and the regular consumption of supplementary vitamins (p<0/05). Conclusion: Although prevalence of malnutrition in this study was lower than WHO statistic report, (30%) but this is locally important and health staff and parents must be educated on nutritional values. Malnutrition is a major problem that is a reason for suppressed immune system, causing the increase of infectious diseases and infant mortality.