Waterborne disease outbreaks (WBDO) of acute gastrointestinal illness (AGI) are a public health concern in France. Their occurrence is probably underestimated due to the lack of a specific surveillance system. The French health insurance database provides an interesting opportunity to improve the detection of these events. A specific algorithm to identify AGI cases from drug payment reimbursement data in the health insurance database has been previously developed. The purpose of our comparative study was to retrospectively assess the ability of the health insurance data to describe WBDO. Data from the health insurance database was compared with the data from cohort studies conducted in two WBDO in 2010 and 2012. The temporal distribution of cases, the day of the peak and the duration of the epidemic, as measured using the health insurance data, were similar to the data from one of the two cohort studies. However, health insurance data accounted for 54 cases compared to the estimated 252 cases accounted for in the cohort study. The accuracy of using health insurance data to describe WBDO depends on the medical consultation rate in the impacted population. As this is never the case, data analysis underestimates the total number of AGI cases. However this data source can be considered for the development of a detection system of a WBDO in France, given its ability to describe an epidemic signal.