Available data in Uganda indicate a resurgence of malaria morbidity and mortality countrywide. This study assessed the burden of malaria, treatment and prevention practices in order initiate a policy debate on the scaling-up of current interventions. A triangulation of methods using a cross-sectional survey and key informant interviews was used to assess self-reported malaria at a household level in Mukono District, Uganda. A total of 5583 households were surveyed, and a high proportion (2897, 51.9%) reported a person with malaria two weeks prior to the survey. Only 546 households (9.8%) owned and used insecticide-treated nets (ITNs) for malaria prevention. Similarly, only a few households (86, 1.5%) used indoor residual spraying. Self-treatment with home-stocked drugs was high, yet there was low awareness of the effectiveness of expired drugs on malaria treatment. Self-reported malaria was associated with socioeconomic, behavioural and environmental factors, but more especially with household ownership of ITNs. These results will contribute to the current debate on identifying new approaches for scaling-up prevention interventions and effective case management, as well as selection of priority interventions for malaria control in Uganda.