The epidemiology of malaria in Eastern Highlands Province (EHP) is characterized by generally very low-level or no local malaria transmission but a considerable risk of epidemics. In non-epidemic situations, parasite prevalence was under 5% in all but one area, Lufa Valley, where P. vivax was the most common parasite (prevalence rate of 58%). During epidemics, however, 23% (range 8-63%) of people were infected, with P. falciparum the predominant parasite. Mixed infections were very common (12%) but P. malariae and P. ovale were rare. Outside epidemics, malaria was only a minor source of febrile illness and enlarged spleens and anaemia (haemoglobin level < 7.5 g/dl) were virtually absent. However, epidemics were associated with a high incidence of relatively severe morbidity, both in terms of fevers and moderate to severe anaemia. Epidemic prevention, surveillance and response therefore are priorities in malaria control in EHP.