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Purpose Famines and food shortages are one of the most common long time histories of Ethiopia. Hence, malnutrition has been persisted at alarming raters in the country. Moreover, it is a major cause of morbidity and mortality in Afar National Regional State of Ethiopia. Specifically, in Amibara and Awash Fentale districts. The anthropometric data were presented on height, weight, MUAC, weight/height/Age and Body Mass Index (BMI) of under-five children. Methods A cross-sectional descriptive survey was conducted from March 01, 2017 to June 15, 2018. The data was collected by using anthropometric measurement. A multi stage random sampling procedure was applied in order to recruit the required sample size. The data collections were conducted at two selected districts in Afar region by trained interviewers and health care providers. The data were analyzed by using SPSS Version 23. Bivariate analysis between dependent and independent variables was employed. Multivariate analysis was also done to control for possible confounding variable by selecting variable which show statistically significant association (P Results Out of 410 under five children's anthropometric finding, the majorities (62.7%) of those registered under five children were male and (33.3%) were female. The majority (46.8%) of under five children were less than or equal to 50 cm by their height. Most (54.1%) of under five children were less than or equal to 12.5 cm by their MUAC. It indicated that they were diagnosed with severe malnutrition based on anthropometric measurements. Meanwhile, majority (64%) of under five children were less than 60% their weight/age. Regression analysis result indicated that all of the variables were not significant predictors of BMI for under five children (P> 0.05). Based on ANOVA result, there was significant difference between sex and other predictors (P= 0.031). This finding implies that improvement in food aid and poverty alleviation programs are very important. Based on the finding, it is important to provide high quality and quantity of food. Moreover, less access to assets and health services commonly contributed for malnutrition. Highlighting under five children's malnutrition will help to develop and design future policies and programs in Ethiopia.