Surveys for Mansonella perstans infection and potentially related clinical manifestations were undertaken in two endemic communities in Mukono and Luwero districts of Uganda where no other human filarial infections are transmitted. A sensitive and accurate counting chamber method was used for quantifying microfilaraemia in 100microl of finger-prick blood. Among 575 and 991 examined individuals aged >or=1 year in the two communities, the overall microfilariae (mf) prevalence was significantly higher in Mukono (76.5%) than in Luwero (57.7%). As early as age 1-4 years, 40.6% and 20.5% of the children were mf-positive. Prevalences increased rapidly with increasing age to reach 89.2% and 81.4% in the 15-19 years age group and then remained high in subsequent age groups. The geometric mean mf intensity among mf-positive individuals was slightly higher in the Mukono community (32.4mf/100microl) than in the Luwero community (29.9mf/100microl), and this parameter increased with age in both communities. No obvious associations were observed between various clinical parameters and M. perstans microfilaraemia in any of the study communities. The observed patterns of microfilaraemia and the lack of obvious visible clinical manifestations suggest that the host's regulatory responses are downregulated in M. perstans infections. [ClinicalTrials.gov identifier: NCT00215280].