Data from the Inter-Regional Health Insurance Information System (SNIIRAM) represent a unique resource for advancing the epidemiology of waterborne, fecal-oral infectious diseases in France. Hospitalized cases of acute gastroenteritis (AGE), accounting for an average of 32% of all AGE cases, can thus be identified based on the content of medical prescriptions and linked to the specific date and municipality. Cases of AGE contracted outside the place of residence (tourists, etc.) can be identified based on the distance between the patient’s municipality of residence and the municipality where care was prescribed. Missing data primarily concern the patient’s municipality of residence (3.3% rate of missing or erroneous data in 2014) and the physician’s practice (7.3%), which can, however, be substituted with the pharmacy where the medications were dispensed (0.3%). The data are nearly complete at four months, but their completeness is sufficient at two months (99%) to assess the impact of epidemics. This report provides the user with a description of the data and the processes involved in their collection and validation, some statistical benchmarks on the resulting incidence indicators, as well as detailed information on their potential and limitations for use. The publication of this document was accompanied by the release of the data for self-service use by the regional intervention units of Santé publique France.