This work aimed to evaluate the usefulness of the French national health insurance information system (SNIIRAM) for implementing epidemiological surveillance of malaria. We implemented an accurate automated tool able to identify incident malaria cases with similar result to those of the French National center of reference for malaria. It allowed working on population living in France as a whole, including sub-populations poorly covered by existing surveillance methods, but the long latency of SNIIRAM data availability does not permit early alert.