OBJECTIVES: The deployment of new antimalarials in Africa provides an important opportunity to develop systems for pharmacovigilance. To inform strategies for reporting adverse events in Uganda, we investigated local perceptions and experiences with antimalarial treatment, and evaluated existing and potential systems for pharmacovigilance. METHODS: Focus group discussions (FGD) were conducted with community members and health workers from urban and rural Uganda exploring knowledge of fever/malaria, perceptions and expectations of treatment, understanding of adverse effects, and experiences with adverse events. Sessions were recorded, transcribed into English, and analysed using a coding scheme developed from pre-defined topics together with themes emerging from the data. RESULTS: Between April and July 2006, we conducted 25 FGDs; 16 with community members and nine with health workers. All respondents had extensive experience with malaria and its treatment. Community members commonly recognized adverse effects of antimalarial therapy. However, events were uncommonly reported, and certain events were often interpreted as signs of successful treatment. Community members often felt that the costs of reporting or seeking additional care outweighed the potential benefits. Health workers were unfamiliar with formal pathways for reporting, and were deterred by the additional work of reporting and fear of incrimination. Respondents provided suggestions for incentives and methods of reporting, emphasizing that pharmacovigilance should ideally encompass the public and private sector, and the community. CONCLUSIONS: To be successful, pharmacovigilance relying on voluntary reporting will require active participation of patients and health workers. Addressing the costs and benefits of reporting, and providing sensitization, training and feedback will be important.