The term raphe nuclei (functional) denotes a composite midline structure that extends from the caudal medulla to the midbrain of the upper cerebrospinal trunk. It includes all of the raphe nuclei (classical) plus the interfascicular nucleus, the interpeduncular nucleus the rostral linear nucleus of the raphe, the caudal linear nucleus of the raphe, and the nucleus incertus ( Swanson-2004 ). All of the component nuclei are found in the rat ( Swanson-2004 ) and the mouse ( Franklin-2008 ). All except the nucleus incertus are found in the human ( Paxinos-2012 ) and the macaque ( Paxinos-2009a ). Functionally the nuclei are part of the behavioral state system ( Swanson-2004 ).