Stunting is recognised as a major public health problem in Rwanda. We therefore aimed to study the demographic, socio-economic and environmental factors determining the spatial pattern of stunting. A cross-sectional study using the data from the 2014- 2015 Rwanda Demographic and Health Survey and environmental data from external geospatial datasets were conducted. The study population was children less than two years old with their mothers. A multivariate linear regression model was used to estimate the effects of demographic, socio-economic and biophysical factors and a proxy measure of aflatoxins exposure on height-for-age. Also, a spatial prediction map of height-for-age to examine the stunting pattern was produced. It was found that age of child, height of mother, secondary education and higher, a child being male and birth weight were associated with height-for-age. After adjusting for demographic and socioeconomic factors, elevation and being served by a rural market were also significantly associated with low height-for-age in children. The spatial prediction map revealed the variability of height-for-age at the cluster-level that was lost when the levels are aggregated at the district level. No associations with height-for-age were found for exclusive breastfeeding, use of deworming tablets, improved water source and improved sanitation in the study population. In addition to the child and mother factors known to determine height-for-age, our study confirms the influence of environmental factors in determining the height-of-age of children in Rwanda. A consideration of the environmental drivers of anthropometric status is crucial to have a holistic approach to reduce stunting.