Objective: To determine the prevalence of adult malnutrition and associated risk factors in a post-conflict area of northern Uganda. Methods: A cross-sectional community survey was performed from September 2011 to June 2013. All registered residents in Gulu Health and Demographic Surveillance System aged 15 years and older were considered eligible. Trained field assistants collected anthropometric measurements (weight and height) and administered questionnaires with information on sociodemographic characteristics, food security, smoking and alcohol. Nutritional status was classified by body mass index. Results: In total, 2062 men and 2924 women participated and were included in the analyses. The prevalence of underweight was 22.3% for men and 16.0% for women, whereas the prevalence of overweight was 1.5% for men and 7.6% for women. In men, underweight was associated with younger (15-19 years) and older age (>55 years) (P < 0.001), being divorced/separated [odds ratio (OR) = 1.91 (95% confidence interval (CI): 1.21-2.99] and smoking (OR = 2.13, 95% CI: 1.67-2.73). For women, underweight was associated with older age (P < 0.001) and hungry-gap rainy season (May-July) (OR = 1.33, 95% CI: 1.04-1.69). Widowed or divorced/separated women were not more likely to be underweight. No association was found between education, alcohol consumption or food security score and underweight. Conclusions: Our findings are not in line with the conventional target groups in nutritional programmes and highlight the importance of continuous health and nutritional assessments of all population groups that reflect local social determinants and family structures.