BackgroundMalnutrition is the main cause of illness and death in children under the age of five. It affects millions of children worldwide, putting their health and future in jeopardy. Therefore, this study aimed to identify and estimate the effects of important determinants of anthropometric indicators by taking into account their association and cluster effects.MethodThe study was carried out in 10 countries in East Africa: Burundi, Ethiopia, Comoros, Uganda, Rwanda, Tanzania, Zimbabwe, Kenya, Zambia, and Malawi. A weighted total sample of 53,322 children under the age of five was included. Given the impact of other predictors such as maternal, child, and socioeconomic variables, a multilevel multivariate binary logistic regression model was employed to analyze the relationship between stunting, wasting, and underweight.ResultThe study included 53,322 children, and 34.7%, 14.8%, and 5.1% were stunted, underweight, and wasted, respectively. Almost half of the children (49.8%) were female, and 22.0% lived in urban areas. The estimated odds of children from secondary and higher education mothers being stunted and wasted were 0.987; 95% CI: 0.979 – 0.994 and 0.999; 95% CI: 0.995 – 0.999, respectively, times the estimated odds of children from no education mothers. Children from middle-class families were less likely to be underweight than children from poorer families.ConclusionThe prevalence of stunting was higher than in the sub-Saharan Africa region, but the prevalence of wasting and underweight was lower. According to the study's findings, undernourishment among young children under the age of five continues to be a significant public health issue in the East African region. Governmental and non-governmental organizations should therefore plan public health participation focusing on paternal education and the poorest households in order to improve the undernutrition status of children under five. Additionally, improving the delivery of healthcare at health facilities, places of residence, children's health education, and drinking water sources are essential for lowering child undernutrition indicators.