Abstract  While the underlying cause of malaria epidemics in the East African highlands remains a subject of debate, we argue that permissive climatic conditions in the normally cool highlands are required for the epidemics to occur. Analysis of climate data from East Africa suggested that, over the last decade, there has been an increase in the frequency and intensity of anomalies in the mean monthly maximum temperatures. We found an association between rainfall and unusually high maximum temperatures and the number of inpatient malaria cases 3–4 months later. A malaria epidemic prediction model was then constructed.