Encephalitides include a large variety of diseases with high morbidity and mortality. Although the majority of identified pathogens are viruses, the cause of the disease remains unexplained in more than half of the cases despite extensive testing. Neuropathology provides the bases of our understanding of the inflammatory lesions in the central nervous system. Brain biopsy proves to be necessary in cases of unknown etiology, which deteriorate despite treatment. Unexpected pathogens can be uncovered by untargeted transcriptomic analysis, based on deep sequencing of small quantities of pathological brain tissue. Combined with immunohistochemistry and in situ hybridization, using tailored antibodies and probes, this next generation sequencing method opens perspectives in the diagnosis of encephalitides with a high efficiency particularly in, but not limited to, immunocompromised patients.