Pneumonia and malaria are common causes of childhood morbidity and mortality in many developing countries and simple guidelines have been proposed to facilitate their diagnosis by relatively unskilled health workers. We have studied children in The Gambia attending out-patient and under-five clinics with clinically suspected pneumonia (cough or difficulty in breathing and a raised respiratory rate) during periods of high or low malaria transmission. During a period of high malaria transmission, 33% of these children had radiological evidence of pneumonia (with or without malaria parasitaemia) compared to 38% who had malaria parasitaemia, no radiological evidence of pneumonia and no other obvious cause of fever. Corresponding figures during a period of low malaria transmission were 48% and 6% respectively. The clinical overlap between pneumonia and malaria has important implications for case management strategies and evaluation of disease-specific interventions in regions in which both pneumonia and malaria are prevalent.