Objective To examine associations between household-level characteristics and underweight in a post-conflict population.Design Nutritional status of residents in the Gulu Health and Demographic Surveillance Site was obtained during a community-based cross-sectional study, ~6 years after the civil war. Household-level factors included headship, polygamy, household size, child-To-Adult ratio, child crowding, living with a stunted or overweight person, deprived area, distance to health centre and socio-economic status. Multilevel logistic regression models examined associations of household and community factors with underweight, calculating OR, corresponding 95 % CI and intraclass correlation coefficients. Effect modification by gender and age was examined by interaction terms and stratified analyses.Setting Rural post-conflict area in northern Uganda.Subjects In total, 2799 households and 11 312 individuals were included, representing all age groups.Results Living in a female-headed v. male-headed household was associated (OR; 95 % CI) with higher odds for underweight among adult men (2·18; 1·11, 4·27) and girls <5 years (1·51; 0·97, 2·34), but lower odds among adolescent women aged 13-19 years (0·46; 0·22, 0·97). Higher odds was seen for residents living in deprived areas (1·37; 0·97, 1·94), with increasing distance to health services (P-Trend <0·05) and among adult men living alone v. living in an average-sized household of seven members (3·23; 1·22, 8·59). Residents living in polygamous households had lower odds for underweight (0·79; 0·65, 0·97).Conclusions The gender-and age-specific associations between household-level factors and underweight are likely to reflect local social capital structures. Adapting to these is crucial before implementing health and nutrition interventions.