BACKGROUND: Zambia has taken lead in implementing integrated malaria control so as to attain the National Health Strategic Plan goal of "reducing malaria incidence by 75% and under-five mortality due to malaria by 20% by the year 2010". The strategic interventions include the use of long-lasting insecticide-treated nets and indoor residual spraying, the use of artemisinin-based combination therapies (ACT) for the treatment of uncomplicated malaria, improving diagnostic capacity (both microscopy and rapid diagnostic tests), use of intermittent presumptive treatment for pregnant women, research, monitoring and evaluation, and behaviour change communication. Financial barriers to access have been removed by providing free malaria prevention and treatment services. METHODS: Data involving all under-five children reporting at the health facility in the first quarter of 2008 was evaluated prospectively. Malaria morbidity, causes of non-malaria fever, prescription patterns treatment patterns and referral cases were evaluated RESULTS: Malaria infection was found only in 0.7% (10/1378), 1.8% (251378) received anti-malarial treatment, no severe malaria cases and deaths occurred among the under-five children with fever during the three months of the study in the high malaria transmission season. 42.5% (586/1378) of the cases were acute respiratory infections (non-pneumonia), while 5.7% (79/1378) were pneumonia. Amoxicillin was the most prescribed antibiotic followed by septrin. CONCLUSION: Malaria related OPD visits have reduced at Chongwe rural health facility. The reduction in health facility malaria cases has led to an increase in diagnoses of respiratory infections. These findings have implications for the management of non-malaria fevers in children under the age of five years.