We examined the relative contribution of malaria-associated severe anaemia (parasitaemia and haematocrit < or = 15%) to malaria-related morbidity and mortality among children admitted at 2 hospitals in areas with different seasonal patterns of malaria infection in Malawi. The prevalence of malaria-associated severe anaemia was 8.5% among admissions at the hospital in an area with sustained, year-round infection (Mangochi District Hospital [MDH]), compared to 5.2% at the hospital in an area with a fluctuating pattern of infection (Queen Elizabeth Central Hospital [QECH]). Infants at MDH were nearly twice as likely to have malaria-associated severe anaemia as were those at QECH. Parasite density on admission was not related to the risk of severe anaemia at MDH, but it was at QECH. A similar proportion of all deaths was attributed to malaria at MDH (17.5%) and QECH (20.4%). However, malaria-associated severe anaemia accounted for 54% of malaria-related deaths at MDH compared to only 32% at QECH. Malaria-associated severe anaemia contributed significantly to morbidity and mortality at both sites, but its impact was more marked in the area with a sustained pattern of infection. These findings suggest that seasonal fluctuations in malaria infection may contribute to differences in patterns of malaria disease.