BACKGROUND: Temperature, rainfall and humidity have been widely associated with the dynamics of malaria vector population and, therefore, with spread of the disease. However, at the local scale, there is a lack of a systematic quantification of the effect of these factors on malaria transmission. Further, most attempts to quantify this effect are based on proxy meteorological data acquired from satellites or interpolated from a different scale. This has led to controversies about the contribution of climate change to malaria transmission risk among others. Our study addresses the original question of relating meteorological factors measured at the local scale with malaria infection, using data collected at the same time and scale. METHODS: 676 children (6-59 months) were selected randomly from three ecologically different sites (urban and rural). During weekly home visits between December 1, 2003, and November 30, 2004, fieldworkers tested children with fever for clinical malaria. They also collected data on possible confounders monthly. Digital meteorological stations measured ambient temperature, humidity, and rainfall in each site. Logistic regression was used to estimate the risk of clinical malaria given the previous month's meteorological conditions. RESULTS: The overall incidence of clinical malaria over the study period was 1.07 episodes per child. Meteorological factors were associated with clinical malaria with mean temperature having the largest effect. CONCLUSION: Temperature was the best predictor for clinical malaria among children under five. A systematic measurement of local temperature through ground stations and integration of such data in the routine health information system could support assessment of malaria transmission risk at the district level for well-targeted control efforts.