“Malaria is still highly prevalent in Uganda. The Ministry of Health in Uganda estimates that in a given year, at least 12.3 million cases of malaria are reported across the country. The disease is most prevalent among children aged 5 years and below and among pregnant women. The government of Uganda has intervened with several malaria programmes ranging from early detection and treatment of the disease among children as well as the provision of intermittent treatment of malaria among pregnant women. Starting in 2000, the Government of Uganda intensified efforts to provide Insecticide Treated Nets (ITNs) and Long Lasting Insecticide Treated Net (LLIN) as a primary means of preventing malaria. Even with the expansion in malaria control programmes, malaria remained endemic and the government reintroduced Indoor Residual Spraying (IRS) in 2006. This paper sets out to assess the cost effectiveness malaria control programmes in Uganda by comparing LLINs and IRS. Based on demographic data from the 2009 Uganda Malaria Indicator Survey the results show that IRS is significantly more effective in preventing malaria among children aged 5 years and below—with an incremental cost per child covered of US$28 per year and gross cost of US$ 701 per death averted.”