Introduction: Malaria is an important disease, causing high morbidity and mortality, especially in Sub-Saharan Africa. Measuring malaria prevalence using malaria rapid diagnostic tests (mRDTs), particularly among a vulnerable population sub-group, is a vital public health step in discovering effective methods of prevention and control. This study set out to examine the association between “place” and other risk factors with malaria prevalence among Batwa Indigenous People (IP). Methods: An analytical cross-sectional study design was implemented. Two surveys January 2014 (n = 572) and April 2014 (n = 541) involving interviews and testing for malaria using mRDTs were conducted in 10 Batwa settlements where a total of 1113 Batwa of all ages were surveyed and tested. The data were first compiled in MS Excel and then imported and analyzed using STATA ver.14. Descriptive statistics, were generated, followed by bivariable and multivariable regression model analysis to establish associations between the predictor and outcome variables with p ≤ 0.05 considered statistically significant. Results: Overall prevalence was 13.94% (n = 146). There is a significant relationship between settlement (place) and malaria prevalence AOR 11.7, 95% CI (1.38 - 98.93), p-value = 0.02. More males 16.97% (n = 84) tested positive compared to females 11.23% (n = 62) but there was no statistically significant association between gender and mRDT (p-value > 0.005). Children less than 5 years registered high prevalence and there was a significant relationship between age and mRDT (p-value ≤ 0.005). Wealth proxy indicators showed no association with prevalence p-value = 0.390. Season had no association with prevalence (p-value = 0.80). However, the proportion of the day spent in the forest/woodlands was significantly associated with malaria prevalence COR 12.83, 95% CI (1.14 - 143.73) p-value = 0.04. Low elevation was significantly associated with malaria prevalence COR 2.42, 95% CI (1.32 - 4.41), p = 0.004 but sleeping under a net and level of education did not show any association with malaria prevalence. Conclusion: This study highlights the importance of place in predicting malaria prevalence among Batwa Indigenous People a marginalized and remortely located sub-population. This study has shown that place matters in determining malaria prevalence. However, other factors like age, elevation and gender also contribute to malaria prevalence. Batwa have higher prevalence than the national and even non-indigenous
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