Background: Despite claims that the Millennium Development Goals (MDG) targets on access to safe drinking water have been met, many 100 s of millions of people still have no access. The challenge remains how to provide these people and especially young children with safe drinking water. Method: We report a longitudinal study designed to assess the effectiveness of an intervention based on provided treated drinking water in containers on self-reported diarrhoea in children. The intervention was "1001 fontaines pour demain" (1001 F) is a non-governmental not for profit organization (created in 2004 and based in Caluire, France) that helps local entrepreneurs treat package, and sell safe drinking water. Cases and controls were chosen at village and household level by propensity score matching Participants were visited twice a month over six months and asked to complete a diarrhoea health diary. Results: In total 4275 follow-up visits were completed on 376 participants from 309 homes. Diarrhoea was reported in 20.4% of children on each visit, equating to an incidence rate estimate of 5.32 episodes per child per year (95% confidence interval = 4.97 to 5.69). Compared to those drinking 1001 F water, children drinking surface water were 33% (95% CI -1 to 17%), those drinking protected ground water were 62% (95% CI 19 to 120%) and those drinking other bottled water 57% (95% CI 15 to 114%) more likely to report diarrhoea. Children drinking harvested rainwater had similar rates of diarrhoea to Children drinking 1001 F water. Conclusion: Our study suggests that 1001 F water provides a safer alternative to groundwater or surface water. Furthermore, our study raises serious concerns about the validity of assuming protected groundwater to be safe water for the purposes of assessing the MDG targets. By contrast our study provides addition evidence of the relative safety of rainwater harvesting.