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In Ethiopia, 38% of children less than 5 years of age are stunted and 57% are anaemic. Both have a negative impact later in life on physical growth and cognitive development and often coexist. There are few studies in Ethiopia that assessed co-morbid anaemia and stunting (CAS) and context-specific factors associated with it. The objective of this study was to assess the prevalence of CAS, and factors associated with CAS among children aged 2 to 5 years, in southern Ethiopia. A community-based cross-sectional survey was conducted among