There is an innate immune system in the brain. It is inducible in a transient manner from the structures that are devoid of blood brain barrier and thereafter within parenchymal microglia during systemic infection. Transcriptional activation of genes encoding proteins of the innate immunity also takes place in diseases of the central nervous system. This recent discovery raised the hypothesis that inflammation and innate immunity may be involved in the etiology of neurodegenerative disorders. Nevertheless, this system is able to trigger the release of neurotrophic factors and to protect neuronal elements during brain infection and trauma. The innate immune response may play a critical role in protecting neurons and be a possible cause of neurodegeneration. The fate of this newly identified cascade of events is therefore likely to have a determinant impact on the central nervous system during infection and injury.