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Background: In May 2012, an outbreak of viral hepatitis A was reported to the Guangxi Center for Disease Control and Prevention from a middle school in Liujiang County. An investigation was conducted to identify the cause and mode of transmission and to recommend control and prevention measures.Methods: A case was defined as any person from the middle school with onset of fatigue, anorexia, abdominal pain, diarrhoea or jaundice from 20 February to 20 May 2012. We compared attack rates (AR) between boys and girls, assuming that only boys used well water and girls used pipeline water. We then selected 133 students from three classes in each of the three grades to compare AR by reported water source and drinking history.Results: There were 22 cases, an AR of 3.8% (21/553) for students and 1.5% for teachers (1/65). Those who used well water were 8.7 (95% confidence interval [CI] = 2.1–37.2) times more likely to be ill than those using pipeline water. The cohort study showed that students who reported using well water daily were 5.2 (95% CI = 0.7–41.8) times more likely to be ill than those that reported using the pipeline water daily. Eighteen cases were confirmed as hepatitis A.Conclusion: This hepatitis A outbreak was potentially caused by a contaminated school well. We recommended that the school discontinue using the well and that the students should drink boiled water. As there is a vaccine for hepatitis A, we recommended that several doses of the vaccine be stored for controlling outbreaks and for immunizing susceptible populations in future outbreaks.