Child malnutrition is one of the major public health problems in Ethiopia. Although most of the previous studies have investigated the problem in relation to social, economic, and demographic variables, the difference in nutritional status across different household types is not explored. Hence, this study assessed the effects of household structure on children’s nutritional status in Ethiopia using data obtained from 8827 children sampled in the 2004 National Welfare Monitoring Survey. The results revealed that children in single parent nuclear households were more vulnerable to malnutrition than those in two-parent nuclear and extended households. The persistent disadvantageous position of single parent nuclear households that did not have access to high child caring capacity and welfare support unveiled that lack of resources (i.e. financial, material, and labour) within the household is associated with poor nutritional status of children. Children’s nutritional status improved with increase in the educational level of mothers. On the other hand, the likelihood of stunting increased with increase in the number of under-five siblings. Thus, household structure affects the nutritional status of children through the mediating effects of socio-economic and demographic factors, indicating the importance of socio-economic support to poor households to address problems of children’s malnutrition.