The response of the brain to systemic infection is physiologically triggered by an activating signal that is mediated by three pathways. 1) The neural pathway that requires activation of primary afferent nerves, such as the vagal or the trigeminal nerves, by involving peripherally produced pathogen-associated molecular patterns (PAMPs) and cytokines. 2) The humoral pathway involves circulating cytokines. They reach the brain at the level of the choroid plexus and the circumventricular organs that lie outside the blood–brain barrier (BBB). 3) The blood–brain barrier alterations induced by the activation of cerebral endothelial cells results in the release of various mediators into the brain. This activation is due to the production, at the early phase of sepsis, of nitric oxide synthase-derived nitric oxide. All of these pathways instigate the activation of microglial cells, which are the resident immune cells of the brain. When activated, microglial cells may negatively affect the brain by the production of nitric oxide, cytokines, and reactive oxygen species that lead to cell death within vulnerable areas of the brain. This production is, in itself, responsible for an increase of the BBB alterations, thus causing a vicious circle of increasing brain dysfunction and injury. These mechanisms are compounded by common metabolic disturbances that occur in septic patients (such as prolonged hyperglycemia, severe hypoxemia), hemodynamic failure, use of medications, and iatrogenic and environmental factors. Septic-associated brain dysfunction may be associated with neurologic sequelae in survivors, including functional and cognitive decline, probably by neurodegenerative and/or ischemic mechanisms.