To understand people's perceptions of malaria and their implications for control programmes, we held focus group discussions (FGDs) and conducted semi-structured interviews (SSIs) with community members in Mbarara, Uganda. Mosquitoes were perceived as the cause or transmitters of malaria but the causation/transmission model of people differed from biomedical facts. Convulsions, a common complication of malaria, were perceived as a supernatural ailment, best treated by traditional medicine, as was splenomegaly. More than 70% of the patients with malaria had treatment from non-public health sources. This included self-treatment (13%), use of traditional healers (12%) and use of private medical practitioners/pharmacists (69%). Although 26% (887/3309) used bednets to prevent malaria, only 7% of the nets were impregnated with insecticide. People who did not use bednets cited discomfort because of heat/humidity and their high cost as reasons. To improve malaria control in this area, people need to be educated on the connection between mosquitoes and malaria and on seeking biomedical treatment for convulsions. The malaria control programme could collaborate with traditional and private health care providers to increase promotion of insecticide-impregnated mosquito nets.