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Undernutrition is a global public health challenge. In Somalia, undernutrition is chronic with the situation often graded for emergency response. The purpose of this study was to provide contextual evidence regarding trends of prevalence and predictors of undernutrition in South Central Somalia. Following the UNICEF conceptual framework of determinants of undernutrition, the study examined which individual, household, and society factors were associated with undernutrition. Using secondary data from cross-sectional nutritional surveys implemented by the Somalia Food Security and Nutrition Analysis Unit from 2007 to 2012, a sample of 75,756 and 60,856 children aged 6-59 months was used in analyzing trends in prevalence and predictors of undernutrition respectively. Linear regression was used to examine trends, while Generalized Estimation Equations were used to determine predictors of undernutrition. Results of this study showed that from 2007 to 2012, there was a declining trend in the prevalence of stunting (R2 = 0.73; p < 0.05) while there was no significant trend in terms of underweight and wasting. When individual, household, and society factors were considered simultaneously, diarrhea, child gender, diet diversity, and minimum meal frequency were significant predictors of underweight; child gender and meal frequency significantly predicted stunting while wasting was significantly predicted by diarrhea, malaria, and diet diversity. Geographical region and livelihood system were significant predictors of undernutrition. The study findings provide evidence to inform nutrition policy and programs that could result in eliminating disparities in child nutrition and reducing undernutrition, ultimately improving survival and development of children in Somalia.