The National Malaria Control Programme (NMCP), organized within the Ministry of Health (MoH), is an essential component for the planning, execution and coordination of malaria control activities. As effective case management remains the mainstay of malaria control in almost every African country, antimalarial drug resistance is a major barrier to the implementation of effective malaria control policies. In order to function effectively, these units must have an efficient surveillance system which can provide reliable and current estimates of the severity of drug resistance. Without this information, it is impossible for the MoH to design and promote a rational antimalarial policy, but because of limited resources, especially of people and expertise, most NMCPs have been unable to initiate and manage such a system. The need for collaborative partnerships between the MoH and the research community prompted the establishment of the East Africa Network for Monitoring Antimalarial Treatment (EANMAT). EANMAT has attempted to bring together the complimentary skills of malaria researchers and MoH staff in four east African countries. After 3 years of operation, data generated by EANMAT have been used to review and modify national malaria treatment policies in Kenya, Uganda, Rwanda and Tanzania. This new approach, which forges a closer working relationship between the research and policy communities, has effectively built capacity around the complex of surveillance, interpretation and use of evidence within a policy environment. The added-value of this approach is that the research community has learned to appreciate the constraints of policy development, and that the control community has established the need to build capacity and ownership of research evidence. Networks similar to EANMAT should be encouraged elsewhere in Africa to engender similar partnerships: to assist the development of rational treatment policies, and thus more effective malaria chemotherapy leading to significant lowering of malaria morbidity and mortality.