BACKGROUND Over the past two decades, Rwanda has experienced impressive economic growth, resulting in considerable improvements in living standards and poverty reduction. Despite these gains, progress on reducing the level of stunting in smallholder rural children, particularly boys, continues to be a serious concern. METHODS Policies, dietary diversity and socio-economic factors that may influence stunting in rural Rwandan children were evaluated using a logit model with clustered variance-covariance estimators based on village membership of the household. RESULTS Stunting of rural children was found to be multidimensionally related to the child's gender, weight and age; the dietary diversity, marriage status and education level of the head of household; mother's height; presence of a family garden or if they owned livestock; environmental factors such as altitude and soil fertility and location relative to a main road en route to a market; and a policy that promoted food production. CONCLUSIONS Findings suggest that agricultural policies may be subsidizing poor dietary behavior in that the aggregation of production encourages households to sell high quality nutritious food such as fruit and vegetables, for more voluminous amounts of nutritionally substandard goods, hence low dietary diversity. However, it is less clear if rural food markets are capable of supplying diverse and nutritious foods at affordable prices on a consistent basis, resulting in a lack of diversity and hence, low nutrient quality diets. Rwanda's next round of food security policies should focus on nutrition insecurity with special emphasis on the lack of protein, micronutrients and calories. Multipronged policies and programs focused on income growth, food security, enhanced access to markets and gender-related nutrition risks from inception through 2 years of age in the rural areas are required to improve rural household health outcomes, stunting in particular.