Background: Use of indoor residual spraying (IRS), long-lasting insecticidal nets (LLINS) and treatment with artemisinin-based combination therapy (ACT) have been greatly promoted in northern Uganda but the region still records highest number of malaria cases with prevalence up to 63%. This study assesses household predicators of malaria in the region and its impact on incidence of malaria at household levels.Methods: A cross-sectional study was conducted in four districts of Gulu, Oyam, Kitgum and Agago covering sixteen known hyper-endemics villages with high malaria burden in northern Uganda. In total, 193 households were surveyed. Data was collected through pre-tested structured questionnaires and systematically coded and analyzed using R software.Results:Women headed 58% of the 193 households surveyed. Six hundred and five (605) individuals were declared to have spent a night in the 193 households surveyed. Nighttime is when mosquitoes mostly gain access to victims in the study area. On average, there were two bed nets per household and out of the 605 individuals declared, 502 502 (86%) spent the night prior to interview under a bed net. Despite this effort, these households still reported malaria incidences in the last three months. Overall, children were prone to malaria more than adults by a ratio of 3:2, and in general, malaria incidences were strongly related to lack of bed nets or use thereof, and also linked directly to the number of individuals in a house. Households without bed nets controlled malaria by means of IRS in combination with closing doors (with the hope of keeping mosquitos at bay), draining stagnant water pool where mosquitos lay their eggs, trimming mosquito covers (grass) around homestead and/or receiving treatment after malaria incidences. When given a choice between insecticides (IRS) and treated bed nets, 1 in 3 households preferred treated bed nets. At the same time, bed nets were perceived unnecessary once IRS was applied. If true, the driving force to spraying insecticides indoor then becomes lack of a bed net. Conclusions:Household predicators of incidence of malaria in northern Uganda includes bed nets, use of treated bed nets, and indoor residual spraying with households not practicing any of these bearing the heaviest burden of malaria. Hierarchical clustering on principal components (HCPC) clusters households into four types in northern Uganda, 1) household that use bed nets and sleep in houses sprayed with insecticides; 2) households that use bed nets but no indoor residual spraying with insecticides; 3) households that have no bed nets and no indoor residual spraying; and 4) test bed nets before use. An opportunity therefore arises for tailoring malaria messages to fit each cluster of households given that clustering here appears not to be random. Malaria incidence was higher in children as compared to the adults that necessities having guidelines for management of interventions in local community setting.