As highland regions of Africa historically have been considered free of malaria, recent epidemics in these areas have raised concerns that high elevation malaria transmission may be increasing. Hypotheses about the reasons for this include changes in climate, land use and demographic patterns. We investigated the effect of land use change on malaria transmission in the south-western highlands of Uganda. From December 1997 to July 1998, we compared mosquito density, biting rates, sporozoite rates and entomological inoculation rates between 8 villages located along natural papyrus swamps and 8 villages located along swamps that have been drained and cultivated. Since vegetation changes affect evapotranspiration patterns and, thus, local climate, we also investigated differences in temperature, humidity and saturation deficit between natural and cultivated swamps. We found that on average all malaria indices were higher near cultivated swamps, although differences between cultivated and natural swamps were not statistically significant. However, maximum and minimum temperature were significantly higher in communities bordering cultivated swamps. In multivariate analysis using a generalized estimating equation approach to Poisson regression, the average minimum temperature of a village was significantly associated with the number of Anopheles gambiae s.l. per house after adjustment for potential confounding variables. It appears that replacement of natural swamp vegetation with agricultural crops has led to increased temperatures, which may be responsible for elevated malaria transmission risk in cultivated areas.