Summary Objective To describe the pattern of fever-associated morbidity, treatment-seeking behaviour for fever episodes, and cause-specific mortality in young children of a malaria-holoendemic area in rural Burkina Faso. Methods In a longitudinal community-based intervention study, 709 representative children aged 6–31 months were followed daily over 6 months (including the main malaria transmission period) through village-based field staff. results Of 1848 disease episodes, 1640 (89%) were fever episodes, and of those, 894 (55%) were attributed to malaria (fever + ≥5000 parasites/μl). Eighty-five percent of fever episodes were treated, mainly with chloroquine and paracetamol, 69% of treatments took place in households, 16% in local health centres, 13% in villages, and 1% in hospitals. Treatment-seeking in a health centre or hospital was associated with accessibility and disease severity. Cerebral malaria and malnutrition-associated diarrhoea were the most frequently diagnosed causes of death. While most children with a post-mortem diagnosis of diarrhoea had not received any treatment, children who died of malaria had often received insufficient treatment. In particular, there was a lack of an appropriate second-line treatment at formal health services after chloroquine treatment had failed to resolve symptoms. conclusions These findings call for more effective prevention and treatment of malaria, malnutrition and diarrhoea in rural African communities, as well as for better supervision of existing malaria treatment guidelines in formal health services.