Context: Children’s health is one of the priorities in most societies. Nevertheless, the highest prevalence rate of malnutrition occurs among under five-year-old children worldwide. Objectives: The aim of this study was to estimate the rate of malnutrition in Iranian children through a systematic review and meta-analysis. Also we tried to identify the most prevalent factors causing malnutrition. Data Sources: The required data were collected by searching the keywords of nutrition, malnutrition, under-nutrition, prevalence, epidemiology, etiology, occurrence and Iran in PubMed, Google Scholar, Scopus, Index Copernicus, DOAJ, EBSCO-CINAHL, SID, Magi-ran and Iranmedex. Results: Twenty studies were selected for the final analysis stage, dating from 1999 to 2014. Number of children investigated for wasting, stunting and underweight was 53612, 54312 and 55012 respectively. The results showed that the prevalence of each type of malnutrition, in terms of wasting, stunting and underweight were 7.8% (95% CI: 4.8%-12.6%), 12.4% (95% CI: 8.3%-18.5%) and 10.5% (95% CI: 7.1%-15.4%), respectively. Parents’ educational level, in particular mothers’, gender, birth weight, the place of residence, and mother’s occupation were mentioned as important factors causing malnutrition. Conclusion: The rate of malnutrition in Iran’s under five-year-old children is lower than the average of that in world and the Eastern Mediterranean region. Breastfeeding, the proper use of complementary feeding, and the principled spacing between births and improving the quality of maternal care have important role in prevention of malnutrition.