Malaria remains an important public heath concern in Nigeria because of its impact on child and maternal health, but the contribution of severe malaria to morbidity among Nigerian children was scantly reported. This study was undertaking to document the hospital-burden of severe malaria among children in Ibadan in order to reflect on the impacts and health implications of the current malaria control strategies. A review of 6-year case records of all children admitted to the emergency ward of the University College Hospital Ibadan was carried out. Cases of severe malaria were defined as those children in whom parasitaemia were confirmed with blood film microscopy and any of the WHO case definitions for severe malaria was documented. Severe malaria cases constituted 11.3% of 16 031 admissions (2000-05) with 89.1% being children <5 years old. Cerebral malaria accounted for about one-fifth (19.7%) of all severe malaria cases. The yearly proportional morbidity rate from severe malaria ranged from 8.7% to 13.2% with significant increase from 2000 to 2004 (X2 = 48.49; df = 5; P < 0.001). Severe malaria accounted for 12.4% of all paediatric deaths with an estimated overall case fatality rate of 9.6%. Deaths from malaria were significantly associated with wasting (Z-score for weight-for-height <or=2.0), age <2 years, hypoglycaemia and respiratory distress. Our data demonstrated an increased trend in morbidity from severe malaria over the study period. Severe malarial anaemia was a more common complication of Plasmodium falciparum malaria than cerebral malaria in hospitalized Nigerian children and it was associated with a high number of deaths. The consequences of high rate of severe malaria may be beyond health as it also affects the economy and the developmental prospects of the country. There may therefore a need to review the current strategies for malaria control in Nigeria.