OBJECTIVE: To determine the cost effectiveness of selected malaria control interventions in the context of reaching the millennium development goals for malaria. DESIGN: Generalised cost effectiveness analysis. DATA SOURCES: Efficacy data came from the literature and authors' calculations supported by expert opinion. Quantities for resource inputs came from the literature and from expert opinion; prices came from the WHO-CHOICE database. METHODS: Costs were assessed in year 2000 international dollars, and effects were assessed as disability adjusted life years averted by a 10 year implementation programme. Analysis was restricted to sub-Saharan regions where the most deadly form of malaria, Plasmodium falciparum, is most prevalent. The impact on population health for various interventions, and their combinations, was evaluated at selected coverage levels by using a state-transition model. Sensitivity analysis was done for age weights and discounting. RESULTS: High coverage with artemisinin based combination treatments was found to be the most cost effective strategy for control of malaria in most countries in sub-Saharan Africa. CONCLUSIONS: A much larger infusion of resources than those currently available is needed to make headway in the fight to roll back malaria. On cost effectiveness grounds, in most areas in sub-Saharan Africa greater coverage with highly effective combination treatments should be the cornerstone of malaria control. However, treatment alone can achieve less than half the total benefit obtainable through a combination of interventions-scaling up the use of impregnated mosquito nets or indoor spraying with insecticides is also critical. Intermittent presumptive treatment of pregnant women can bring a small but important additional health gain at relatively low cost.