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<p>Abstract</p> <p>Background</p> <p>Amongst school-aged children living in malaria endemic areas, chronic morbidity and exacerbation of morbidity associated with other infections are often not coincident with the presence or levels of <it>Plasmodium </it>parasitaemia, but may result from long-term exposure to the parasite. Studies of hepatosplenomegaly associated with <it>Schistosoma mansoni </it>infection and exposure to <it>Plasmodium </it>infection indicate that differences that occur over 1–2 km in levels of <it>Plasmodium </it>transmission are related to the degree of exacerbation of hepatosplenomegaly and that <it>Plasmodium falciparum </it>schizont antigen (Pfs)-IgG3 levels may be a marker for the differing levels of exposure.</p> <p>Methods</p> <p>To investigate the validity of Pfs-IgG3 measurements as a tool to assess these comparative exposure levels on a microgeographical scale, cross-sectional community surveys were conducted over a 10 × 6 km study site in Makueni District, Kenya, during low and high malaria transmission seasons. During both high and low malaria transmission seasons, thick blood smears were examined microscopically and circulating Pfs-IgG3 levels measured from dried blood spot elute. GIS techniques were used to map prevalence of parasitaemia and Pfs-IgG3 levels.</p> <p>Results</p> <p>Microgeographical variations in prevalence of parasitaemia were observed during the high but not the low transmission season. Pfs-IgG3 levels were stable between high and low transmission seasons, but increased with age throughout childhood before reaching a plateau in adults. Adjusting Pfs-IgG3 levels of school-aged children for age prior to mapping resulted in spatial patterns that reflected the microgeographical variations observed for high season prevalence of parasitaemia, however, Pfs-IgG3 levels of adults did not. The distances over which age-adjusted Pfs-IgG3 of school-aged children fluctuated were comparable with those distances over which chronic morbidity has previous been shown to vary.</p> <p>Conclusion</p> <p>Age-adjusted Pfs-IgG3 levels of school-aged children are stable and when mapped can provide a tool sensitive enough to detect microgeographical variations in malaria exposure, that would be useful for studying the aetiology of morbidities associated with long-term exposure and co-infections.</p>