Lack of access to safe water and sanitation contributes to diarrhoea moribidity and mortality in developing countries. We evaluated the impact of household water treatment, latrines, shallow wells, and rainwater harvesting on diarrhoea incidence in rural Kenyan children. We compared diarrhoea rates in 960 children aged <5 years in 556 households in 12 randomly selected intervention villages and six randomly selected comparison villages during weekly home visits over an 8-week period. On multivariate analysis, chlorinating stored water [relative risk (RR) 0·44, 95% confidence interval (CI) 0·28–0·69], latrine presence (RR 0·71, 95% CI 0·54–0·92), rainwater use (RR 0·70, 95% CI 0·52–0·95), and living in an intervention village (RR 0·31, 95% CI 0·23–0·41), were independently associated with lower diarrhoea risk. Diarrhoea risk was higher among shallow well users (RR 1·78, 95% CI 1·12–2·83). Chlorinating stored water, latrines, and rainwater use all decreased diarrhoea risk; combined interventions may have increased health impact.