Based on data generated from 180 randomly selected households with children age under five years old in Aysaita district of Afar region of Ethiopia, this study explored prevalence of malnutrition and scrutinized household characteristics, maternal characteristics, specifics of the child and economic variables associated with child malnutrition. The height-for-age Z-scores (HAZ), weight-for-height Z-scores (WHZ) and weight-for-age Z-scores (WAZ) were used to measure the extent of stunting, wasting and underweight, respectively. The results revealed that prevalence of long term nutritional imbalance and malnutrition status indicator (i.e. stunting) was 67.8%. The short term measure (wasting) was found to be 12.8% and underweight was found to be 46.1%. Moreover, children in households which are headed by women, and characterized by more dependency ratio, less access to assets, health services and institutions are more likely to be undernourished.