Pharmacovigilance, defined as "the science and activities relating to the detection, assessment, understanding and prevention of adverse effects or any other possible drug related problem", is increasingly being recognized in Africa. Many African countries have simultaneously adopted artemisinin derivative based combination therapy (ACT) as first-line treatment for uncomplicated malaria, offering an opportunity to assess the safety of these drugs when used widely. While ACTs appear to be safe and well-tolerated, there is little experience with these medicines in Africa, outside clinical trials. Pharmacovigilance for ACTs and other combination treatments in Africa is essential. Malaria transmission intensity is high and antimalarial medicines are used frequently. Presumptive treatment of fever with antimalarials is common, often in the absence of a confirmed diagnosis, using drugs obtained without a prescription. Informal use of antimalarial drugs may increase the risk of incorrect dosing, inappropriate treatment, and drug interactions, which may impact negatively on drug safety. Furthermore, the administration of antimalarial treatments in patients with a concomitant illness, including HIV/AIDs, tuberculosis and malnutrition, is a concern. African countries are being encouraged to establish pharmacovigilance systems as ACTs are rolled out. However, pharmacovigilance is difficult, even in countries with a well-developed health care system. The rationale for pharmacovigilance of antimalarial drugs is discussed here, outlining the practical challenges and proposing approaches that could be adopted in Africa.