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Background: The indigenous Batwa of southwestern Uganda are among the most highly impoverished populations in Uganda, yet there is negligible research on the prevalence of malaria in this population. Plasmodium falciparum malaria parasitaemia prevalence was estimated in an indigenous Batwa and a non-indigenous neighbouring population, and an exploration of modifiable risk factors was carried out to identify potential entry points for intervention. Additionally, evidence of zooprophylaxis was assessed, hypothesizing that livestock ownership may play a role in malaria risk. Methods: Two cross-sectional surveys of Batwa and non-Batwa communities were carried out in Kanungu District, Uganda in July 2013 and April 2014 based on a census of adult Batwa and a two-stage systematic random sample of adult non-Batwa in ten Local Councils where Batwa settlements are located. A community-based questionnaire and antigen rapid diagnostic test for P. falciparum were carried out in the cross-sectional health surveys. A multivariable logistic regression model was built to identify risk factors associated with positive malaria diagnostic test. A subset analysis of livestock owners tested for zooprophylaxis. Results: Batwa experienced higher prevalence of malaria parasitaemia than non-Batwa (9.35 versus 4.45 %, respectively) with over twice the odds of infection (OR 2.21, 95 % CI 1.23-3.98). Extreme poverty (OR 1.96, 95 % CI 0.98-3.94) and having an iron sheet roof (OR 2.54, 95 % CI 0.96-6.72) increased the odds of infection in both Batwa and non-Batwa. Controlling for ethnicity, wealth, and bed net ownership, keeping animals inside the home at night decreased the odds of parasitaemia among livestock owners (OR 0.29, 95 % CI 0.09-0.94). Conclusion: A health disparity exists between indigenous Batwa and non-indigenous community members with Batwa having higher prevalence of malaria relative to non-Batwa. Poverty was associated with increased odds of malaria infection for both groups. Findings suggest that open eaves and gaps in housing materials associated with iron sheet roofing represent a modifiable risk factor for malaria, and may facilitate mosquito house entry; larger sample sizes will be required to confirm this finding. Evidence for possible zooprophylaxis was observed among livestock owners in this population for those who sheltered animals inside the home at night. [ABSTRACT FROM AUTHOR]