Background: Under-nutrition contributes to childhood morbidity and mortality, particularly in low-income countries. While Rwanda is one of few countries on track to reduce the prevalence of underweight children under five years old by 50 % from 1990 to 2015 (a target of Millennium Development Goal1), underweight children remain a large public health problem with one out of ten children having low weight-for-age. Methods: We performed a cross-sectional study using 2010 RDHS data on 4177 children under five years of age with weight and height measurements. Children were classified as underweight if their weight-for-age Z scores (WAZs) were <2 standard deviations (SD) and severely underweight if WAZs were <3 SD from the mean of the reference population. We used multivariable logistic regression model to identify child, maternal, and household characteristics associated with being underweight. Results: Eleven percent (469) of the 4177 children sampled were underweight and 2.2 % (90) were severely underweight. After adjusting for possible confounders, we found that children were more likely to be underweight if they were male (OR = 1.42, 95 % confidence interval (CI):1.12, 1.79); had fever in the two weeks prior to survey administration (OR = 1.45, 95 % CI:1.07, 1.97) or were non-singletons compared to first-born singletons (OR = 4.04, 95 % CI:2.12, 7.71). Mothers were more likely to have underweight children if they were over 35 years of age compared to those age 17-24 years (OR = 1.67, 95 % CI:1.04, 2.70); with BMI <18.5 compared to BMI between 18.5 to 24.9 (OR = 2.62, 95 % CI:1.70, 4.04), who had no education or primary education only (OR = 3.56, 95 % CI:1.83, 6.95; OR = 3.49, 95 % CI:1. 87, 6.51, respectively) compared to secondary education or higher, and those who did not have delivery assisted by a skilled provider (OR = 1.33, 95 % CI:1.04, 1.72). Household characteristics associated with underweight children included status in the bottom two wealth quintiles compared to the highest (OR = 1.71, 95 % CI:1.27, 2.30). Conclusion: Rwanda was one of the first countries to achieve Millennium Development Goal1. However, even in light of this success, the prevalence of underweight children remains high. Our analysis of specific child, maternal and household risk factors for under-nutrition may help identify potential interventions to address this remaining burden.