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Background: Ethiopia has low malaria prevalence compared to most other malaria-endemic countries in Africa. However, malaria is still a major public health problem in the country. The binary logistic regression model has been widely used to analyse malaria indicator survey (MIS) data. However, most MIS have a hierarchical structure which may result in dependent data. Since this model assumes that conditional on the covariates the malaria statuses of individuals are independent, it ignores potential intra-cluster correlation among observations within a cluster and may generate biased analysis results and conclusions. Therefore, the aim of this study was to quantify the variation in the prevalence of malaria between sample enumeration areas (SEAs) or clusters, the effects of cluster characteristics on the prevalence of malaria using the intra-class correlation coefficient as well as to identify significant factors that affect the prevalence of malaria using the multilevel logistic regression modelling in three major regions of Ethiopia, namely Amhara, Oromia and Southern Nations, Nationalities and Peoples' (SNNP). Methods: Dataset for three regional states extracted from the 2011 Ethiopian National Malaria Indicator Surveys (EMIS) national representative samples was used in this study. It contains 9272 sample individuals selected from these regions. Various multilevel models with random sample SEA effects were applied taking into account the survey design weights. These weights are scaled to address unequal probabilities of selection within clusters. The spatial clustering of malaria prevalence was assessed applying Getis-Ord statistic to best linear unbiased prediction values of model random effects. Results: About 53.82 and 28.72 per cents of the sampled households in the study regions had no mosquito net and sprayed at least once within the last 12 months, respectively. The results of this study indicate that age, gender, household had mosquito nets, the dwelling has windows, source of drinking water, the two SEA-level variables, i.e. region and median altitude, were significantly related to the prevalence of malaria. After adjusting for these seven variables, about 45% of the residual variation in the prevalence of malaria in the study regions was due to systematic differences between SEAs, while the remaining 55% was due to unmeasured differences between persons or households. The estimated MOR, i.e. the unexplained SEA heterogeneity, was 4.784. This result suggests that there is high variation between SEAs in the prevalence of malaria. In addition, the 80% interval odds ratios (IORs) related to SEA-level variables contain one suggesting that the SEA variability is large in comparison with the effect of each of the variable. Conclusions: The multilevel logistic regression with random effects model used in this paper identified five individual / household and two SEA-level risk factors of malaria infection. Therefore, the public health policy makers should pay attentions to those significant factors, such as improving the availability of pure drinking water. Further, the findings of spatial clustering provide information to health policymakers to plan geographically targeted interventions to control malaria transmission. [ABSTRACT FROM AUTHOR]