Malnutrition is one of the most important health issues in developing countries, which might have adverse effects on the physical and intellectual health of children. The search process was started to find Persian and English articles published until September 2017 regarding the prevalence of malnutrition in children under the age of six in Iran using national and international databases including SID, Magiran, Irandoc, IranMedex, PubMed, Medline, Scopus, and ISI Web of Science. The data were analyzed using meta-analysis methods and the random effects model. The heterogeneity of studies was analyzed using the I
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index. The data were analyzed using R and STATA software (ver. 11.2). Twenty seven articles conducted from 2002 to 2016 were collected to be included in the meta-analysis process. The total sample size was 161,941 patients in an age range of 0-6 years. The final estimate of the prevalence of different forms of malnutrition through meta-analysis of data extracted from studies in Iran was as follows: severe underweight (1%; 95% confidence interval [CI], 1–1), moderate underweight (6%; 95% CI, 5–7), mild underweight (25%; 95% CI, 21–28), severe short stature (3%; 95% CI, 2–3), moderate short stature (8%; 95% CI, 6–9), mild short stature (21%; 95% CI, 17–24), severe slimness (1%; 95% CI, 1–1), moderate slimness (5%; 95% CI, 4–5) and mild slimness (20%; 95% CI, 17–24). Considering that the prevalence of malnutrition is relatively high in Iran, health authorities should plan to improve the nutritional status of children.