Both malaria and protein-energy malnutrition (PEM) are highly prevalent in young children of sub-Saharan Africa, and the association between PEM and malaria continues to be discussed controversially. We analysed the association between PEM, malaria morbidity and all-cause mortality in a cohort of 709 children aged 6-30 months in a malaria holoendemic rural area of Burkina Faso. Study children were followed over the main malaria transmission period (June-December) in 1999 through longitudinal malaria surveillance complemented by three cross-sectional clinical surveys. There was no association between PEM and malaria morbidity, but malnourished children had a more than two-fold higher risk of dying than non-malnourished children.