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Despite better knowledge of pathophysiology and a wider use of new molecular technologies for the diagnosis, the etiological diagnosis of acute encephalitis is not established in most cases. Incidence, prognosis, rate of this disease and severity of sequelae remain unknown. In France, according to the published data, the incidence of encephalitis is estimated to be 1.9 cases per 100 000 inhabitants in average among non-HIV patients. The etiological diagnosis is established in less than 30% of cases. The more frequent diagnosis is herpetic encephalitis in adults and encephalitis caused by Varicella zoster virus in children younger than 16 years. Despite a difficult diagnosis and the lack of specific treatment for most of these infections, the etiological diagnosis should always be deeply explored to precise the individual prognosis, to allow better management of antibiotic therapy, and to improve epidemiological knowledge. We present the recommendations established by the French Society for Infectious Diseases. First designed to suit the French epidemiology, they take in count the possible exposure of patients to different epidemiological patterns. Three levels of etiological tests are proposed, from the most common infections and those, which required an immediate treatment, to the rarest ones.