Knowledge of malaria and treatment-seeking behaviour was investigated in an area of low transmission in Uganda to help health services to plan for appropriate interventions to control malaria. Although knowledge of malaria symptoms, preventive methods and malaria risks was widespread, few were actually using insecticide-treated nets. Many patients (25%) had received treatment prior to visiting a health facility, with drug shops and general stores being the main sources of treatment. Some shops dispensed quinine, a second-line drug recommended for complicated malaria. Prescription practices of health staff often did not comply with guidelines. Only 30% of patients received treatment at a health facility within 24h of onset of symptoms. Findings indicate a need for community-level information campaigns on prompt treatment and introduction of home-based management of fever. Measures are needed to protect second-line drugs from misuse. Failure to comply with drug policy in both the private and public sectors is of concern in an era of rapidly evolving drug policy changes and highlights the need for reorientation and training of health staff and drug vendors to improve malaria diagnostic and treatment skills.