In Indonesia, where diarrhea remains a major cause of mortality among children <5 years, the government promotes boiling of drinking water. We assessed the impact of boiling on water quality in South Sulawesi. We surveyed randomly selected households with at least one child <5 years old in two rural districts and tested source and stored water samples for Escherichia coli contamination. Among 242 households, 96% of source and 51% of stored water samples yielded E. coli. Unboiled water samples, obtained from 15% of households, were more likely to yield E. coli than boiled samples [prevalence ratios (PR) = 2.0, 95% confidence interval (CI) 1.7–2.5]. Water stored in wide-mouthed (PR = 1.4, 95% CI = 1.1–1.8) or uncovered (PR = 1.8, 95% CI = 1.3–2.4) containers, or observed to be touched by the respondent's hands (PR = 1.6, 95% CI = 1.3–2.1) was more likely to yield E. coli. A multivariable model showed that households that did not boil water were more likely to have contaminated stored water than households that did boil water (PR = 1.9, 95% CI = 1.5–2.3). Although this study demonstrated the effectiveness of boiling in reducing contamination, overall impact on water quality was suboptimal. Future studies are needed to identify factors behind the success of boiling water in Indonesia to inform efforts to scale up other effective water treatment practices.

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