Anemia in children under 5 years of age, defined by the World Health Organization as a hemoglobin concentration < 11 g/dL, is a global public health problem. According to the 2006 Demographic Health Survey, the prevalence of anemia among children under five in Uganda was 72% in 2006. The 2009 Uganda Malaria Indicator Survey was conducted in late 2009 and revealed that over 60% of children less than 5 years of age were anemic and that over half of children tested positive for malaria via a rapid diagnostic test. Children with concomitant malaria infection, and in households without any type of mosquito net were more likely to be anemic, confirming that children under 5 years, are vulnerable to both the threat of malaria and anemia and the beneficial effect of malaria prevention tools. However, prevention and treatment of other factors associated with the etiology of anemia (e.g., iron deficiency) are likely necessary to combat the toll of anemia in Uganda.