OBJECTIVE: To estimate the direct burden of malaria among children younger than 5 years in sub-Saharan Africa (SSA) for the year 2000, as part of a wider initiative on burden estimates. METHODS: A systematic literature review was undertaken in June 2003. Severe malaria outcomes (cerebral malaria, severe malarial anaemia and respiratory distress) and non-severe malaria data were abstracted separately, together with information on the characteristics of each study and its population. Population characteristics were also collated at a national level. A meta-regression model was used to predict the incidence of malaria fevers at a national level. For severe outcomes, results were presented as median rates as data were too sparse for modelling. RESULTS: For the year 2000, an estimated 545,000 (uncertainty interval: 105,000-1,750,000) children under the age of 5 in SSA experienced an episode of severe malaria for which they were admitted to hospital. A total of 24,000 (interquartile range: 12,000-37,000) suffered from persistent neurological deficits as a result of cerebral malaria. The number of malaria fevers associated with high parasite density in under-5s in SSA in 2000 was estimated as 115,750,000 (uncertainty interval: 91,243,000-257,957,000). CONCLUSION: Our study predicts a lower burden than previous estimates of under-5 malaria morbidity in SSA. As there is a lack of suitable data to enable comprehensive estimates of annual malaria incidence, we describe the information needed to improve the validity of future estimates.