The last decade has seen an increase in investment and concerted efforts by the Malawi Ministry of Health and partners to control malaria disease. This report summarizes what is known about the burden of malaria and the strategies being implemented to control it in Malawi. Over the past 5 years, roll out of treatment and prevention efforts have been successful in the country, as demonstrated by increased use of insecticide treated nets, improved access to prompt and effective treatment and the initiation of pilot studies of indoor residual spraying. However, unlike other countries in the region, the recent data have not suggested a decrease in the burden of disease. We describe the environment in which the activities of Malawi's International Center for Excellence in Malaria Research (ICEMR) will be carried out and provide the rationale for the clinical, entomological and molecular studies. Our approach is to establish consistent, stainable data collection systems that are embedded within the public health sector. Through standardized and long-term studies of hosts, parasites and vectors, we hope to contribute to assessment of malaria disease burden, the appropriate application of interventions and policies and provide both the data collection and the health care infrastructure to ultimately eliminate the disease.