OBJECTIVE: To explore associations of environmental and demographic factors with diarrhoea and nutritional status among children in Rusizi district, Rwanda. METHODS: We obtained cross-sectional data from 8847 households in May-August 2013 from a baseline survey conducted for an evaluation of an integrated health intervention. We collected data on diarrhoea, water quality, and environmental and demographic factors from households with children <5, and anthropometry from children <2. We conducted log-binomial regression using diarrhoea, stunting and wasting as dependent variables. RESULTS: Among children <5, 8.7% reported diarrhoea in the previous 7 days. Among children <2, stunting prevalence was 34.9% and wasting prevalence was 2.1%. Drinking water treatment (any method) was inversely associated with caregiver-reported diarrhoea in the previous 7 days (PR = 0.79, 95% CI: 0.68-0.91). Improved source of drinking water (PR = 0.80, 95% CI: 0.73-0.87), appropriate treatment of drinking water (PR = 0.88, 95% CI: 0.80-0.96), improved sanitation facility (PR = 0.90, 95% CI: 0.82-0.97), and complete structure (having walls, floor and roof) of the sanitation facility (PR = 0.65, 95% CI: 0.50-0.84) were inversely associated with stunting. None of the exposure variables were associated with wasting. A microbiological indicator of water quality was not associated with diarrhoea or stunting. CONCLUSIONS: Our findings suggest that in Rusizi district, appropriate treatment of drinking water may be an important factor in diarrhoea in children <5, while improved source and appropriate treatment of drinking water as well as improved type and structure of sanitation facility may be important for linear growth in children <2. We did not detect an association with water quality.