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Background  In Uganda, malaria vector control interventions and case management with Artemisinin Combination Therapies (ACTs) have been scaled up over the last few years as a result of increased funding. Data on parasitaemia prevalence among children less than 5 years old and coverage of interventions was collected during the first two Malaria Indicator Surveys (MIS) conducted in 2009 and 2014, respectively. In this study, we quantify the effects of control interventions on parasitaemia risk changes between the two MIS in a spatio-temporal analysis.    Methods  Bayesian geostatistical and temporal models were fitted on the MIS data of 2009 and 2014. The models took into account geographical misalignment in the locations of the two surveys and adjusted for climatic changes and socio-economic differentials. Parasitaemia risk was predicted over a 2 × 2 km 2  grid and the number of infected children less than 5 years old was estimated. Geostatistical variable selection was applied to identify the most important ITN coverage indicators. A spatially varying coefficient model was used to estimate intervention effects at sub-national level.    Results  The coverage of Insecticide Treated Nets (ITNs) and ACTs more than doubled at country and sub-national levels during the period 2009–2014. The coverage of Indoor Residual Spraying (IRS) remained static at all levels. ITNs, IRS, and ACTs were associated with a reduction in parasitaemia odds of 19% (95% BCI: 18–29%), 78% (95% BCI: 67–84%), and 34% (95% BCI: 28–66%), respectively. Intervention effects varied with region. Higher socio-economic status and living in urban areas were associated with parasitaemia odds reduction of 46% (95% BCI: 0.51–0.57) and 57% (95% BCI: 0.40–0.53), respectively. The probability of parasitaemia risk decline in the country was 85% and varied from 70% in the North-East region to 100% in Kampala region. The estimated number of children infected with malaria declined from 2,480,373 in 2009 to 825,636 in 2014.    Conclusions  Interventions have had a strong effect on the decline of parasitaemia risk in Uganda during 2009–2014, albeit with varying magnitude in the regions. This success should be sustained by optimizing ITN coverage to achieve universal coverage.    Electronic supplementary material  The online version of this article (doi: 10.1186/s13071-017-2393-0) contains supplementary material, which is available to authorized users.

The contribution of malaria control interventions on spatio-temporal changes of parasitaemia risk in Uganda during 2009–2014