BackgroundMalaria is one of the major causes of childhood death in sub-Saharan countries. A reliable estimation of malaria prevalence is important to guide and monitor progress toward control and elimination. The aim of the study was to estimate the true prevalence of malaria in children under five in the Democratic Republic of the Congo, Uganda and Kenya, using a Bayesian modelling framework that combined in a novel way malaria data from national household surveys with external information about the sensitivity and specificity of the malaria diagnostic methods used in those surveys—i.e., rapid diagnostic tests and light microscopy.MethodsData were used from the Demographic and Health Surveys (DHS) and Malaria Indicator Surveys (MIS) conducted in the Democratic Republic of the Congo (DHS 2013–2014), Uganda (MIS 2014–2015) and Kenya (MIS 2015), where information on infection status using rapid diagnostic tests and/or light microscopy was available for 13,573 children. True prevalence was estimated using a Bayesian model that accounted for the conditional dependence between the two diagnostic methods, and the uncertainty of their sensitivities and specificities obtained from expert opinion.ResultsThe estimated true malaria prevalence was 20% (95% uncertainty interval [UI] 17%–23%) in the Democratic Republic of the Congo, 22% (95% UI 9–32%) in Uganda and 1% (95% UI 0–3%) in Kenya. According to the model estimations, rapid diagnostic tests had a satisfactory sensitivity and specificity, and light microscopy had a variable sensitivity, but a satisfactory specificity. Adding reported history of fever in the previous 14 days as a third diagnostic method to the model did not affect model estimates, highlighting the poor performance of this indicator as a malaria diagnostic.ConclusionsIn the absence of a gold standard test, Bayesian models can assist in the optimal estimation of the malaria burden, using individual results from several tests and expert opinion about the performance of those tests.Electronic supplementary materialThe online version of this article (10.1186/s12936-018-2211-y) contains supplementary material, which is available to authorized users.