BACKGROUND: Severe malarial anaemia accounts for up to nearly 1 million deaths annually in under-fives in Africa. AIMS: To describe clinical and social indicators of anaemia in under-fives with malaria seeking healthcare at a hospital in northern Cameroon. METHODS: This cross-sectional study included 91 consecutive patients below the age of 60 months in whom malaria was diagnosed by symptomatic fever and microscopic examination. Patients were clinically investigated and mothers questioned on related clinical and social aspects. RESULTS: Anaemia (haemoglobin <110 g/L) was detected in 82% (69/84), and a high parasite load (>100 Plasmodia per 100 high-power fields) in 26% (24/91) of the patients. Clinical findings were associated with the levels of haemoglobin, rather than the parasite load on a single blood slide. Anaemia was found significantly more often in children between the ages of 12 and 23 months and in patients born at home (p=0.035 and p=0.048 respectively). Severe anaemia (haemoglobin <50 g/L) was found significantly more often in patients who had not been vaccinated (p=0.008). CONCLUSIONS: Anaemia is an important health issue in this population. Clinical signs were associated with the haemoglobin status of the patient rather than the parasite load determined by a single blood slide. Recently weaned children and children of mothers with low socio-economic status and who do not usually use the hospital services, may need particular attention in prevention of anaemia. Further studies are required in order to establish cost-effective interventions against anaemia in under-fives in northern Cameroon.