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Abstract Background Rural parts of Mali carry a disproportionate burden of the country’s high under-five mortality rate. A range of household factors are associated with poor under-five health in resource-limited settings. However, it is unknown which most influence the under-five mortality rate in rural Mali. We aimed to describe household factors associated with under-five mortality in Bankass, a remote region in central Mali. Methods We analysed baseline household survey data from a trial being conducted in Bankass. The survey was administered to households between December 2016 and January 2017. Under-five deaths in the five years prior to baseline were documented along with detailed information on household factors and women’s birth histories. Factors associated with under-five mortality were analysed using Cox regression. Results Our study population comprised of 17,408 under-five children from 8322 households. In the five years prior to baseline, the under-five mortality rate was 152.6 per 1000 live births (158.8 and 146.0 per 1000 live births for males and females, respectively). Living a greater distance from a primary health center was associated with a higher probability of under-five mortality for both males (adjusted hazard ratio [aHR] 1.53 for ≥10 km versus