The main objective of this study was to establish the relationship between malaria prevalence and environmental and socio-economic variables. An understanding of the factors that are associated with malaria prevalence is critical for the design of policies aimed at reducing malaria prevalence. Regression results using OLS indicate no relationship between malaria prevalence and environmental and socio-economic variables. There is need for further study using disaggregated data, panel data, and adding more control variables to the health production model to identify the factors that are associated with malaria prevalence in Uganda.