The population of the northern part of the province of KwaZulu Natal in South Africa has experienced low levels of malaria transmission intensity for many years. We investigated the widely held assumption that individuals in this population do not develop clinical tolerance to infection with Plasmodium falciparum. We calculated malaria incidence rates by 5-year age groups from a comprehensive small area malaria reporting system and from national census data for the period from mid-1990 to mid-1999. Incidence rates were plotted against age groups for each of the nine malaria seasons, and by quintile of crude incidence rate. These show that age-specific incidence varied considerably in areas of high incidence and in years of high incidence. In these areas malaria incidence rose with age until the late teens, and either remained constant or decreased in young adults. This finding appears to be consistent with results from settings of much higher transmission intensities which show that clinical tolerance to infection with P. falciparum in adults may be acquired as a result of a small number of infective bites in early childhood and implies that even in this relatively low transmission area, there is an asymptomatic reservoir of infection in older people. The results also show that in high incidence subregions the lowest incidences are reported for children under 5 years of age, which may be the result of greater protection offered to this age group by malaria vector control through indoor house spraying.