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Background: Heterogeneity in malaria transmission has household, temporal, and spatial components. These factors are relevant for improving the efficiency of malaria control by targeting heterogeneity. To quantify variation, we analyzed mosquito counts from entomological surveillance conducted at three study sites in Uganda that varied in malaria transmission intensity. Mosquito biting or exposure is a risk factor for malaria transmission. Methods: Using a Bayesian zero-inflated negative binomial model, validated via a comprehensive simulation study, we quantified household differences in malaria vector density and examined its spatial distribution. We introduced a novel approach for identifying changes in vector abundance hotspots over time by computing the Getis-Ord statistic on ratios of household biting propensities for different scenarios. We also explored the association of household biting propensities with housing and environmental covariates. Results: In each site, there was evidence for hot and cold spots of vector abundance, and spatial patterns associated with urbanicity, elevation, or other environmental covariates. We found some differences in the hotspots in rainy vs. dry seasons or before vs. after the application of control interventions. Housing quality explained a portion of the variation among households in mosquito counts. Conclusion: This work provided an improved understanding of heterogeneity in malaria vector density at the three study sites in Uganda and offered a valuable opportunity for assessing whether interventions could be spatially targeted to be aimed at abundance hotspots which may increase malaria risk. Indoor residual spraying was shown to be a successful measure of vector control interventions in Tororo, Uganda. Cement walls, brick floors, closed eaves, screened airbricks, and tiled roofs were features of a house that had shown reduction of household biting propensity. Improvements in house quality should be recommended as a supplementary measure for malaria control reducing risk of infection.