Boiling is the most common method of household water treatment in developing countries; however, it is not always effectively practised. We conducted a randomized controlled trial among 210 households to assess the effectiveness of water pasteurization and safe-storage interventions in reducing Escherichia coli contamination of household drinking water in a water-boiling population in rural Peru. Households were randomized to receive either a safe-storage container or a safe-storage container plus water pasteurization indicator or to a control group. During a 13-week follow-up period, households that received a safe-storage container and water pasteurization indicator did not have a significantly different prevalence of stored drinking-water contamination relative to the control group [prevalence ratio (PR) 1·18, 95% confidence interval (CI) 0·92–1·52]. Similarly, receipt of a safe-storage container alone had no effect on prevalence of contamination (PR 1·02, 95% CI 0·79–1·31). Although use of water pasteurization indicators and locally available storage containers did not increase the safety of household drinking water in this study, future research could illuminate factors that facilitate the effective use of these interventions to improve water quality and reduce the risk of waterborne disease in populations that boil drinking water.