[2] Selective serotonin reuptake inhibitor (SSRI) antidepressants are believed to act in these nuclei, as well as at their targets.

This study was published before techniques enabling the visualization of serotonin or the enzymes participating in its synthesis had been developed, as first demonstrated by Dahlström and Fuxe in 1964.

The spelling raphe/raphes however can also be contested as numerous sources[12][13][14] indicate that raphe is an incorrect Latin rendering of the Ancient Greek word ῥαφή as the initial letter rho with rough breathing (spiritus asper) is normally rendered as rh in Latin.

The connection between these areas, particularly between the nucleus raphe dorsalis and the orbital cortices, is thought to have influences on depression and obsessive compulsive disorder prognosis.

Many of the neurons in the nuclei (but not the majority) are serotonergic; i.e., contain serotonin, a type of monoamine neurotransmitter and are modulated through fibrous pathways in the midbrain.

[19] Projections from the raphe nuclei also terminate in the dorsal horn of spinal gray matter where they regulate the release of enkephalins, which inhibit pain sensation.

The SCN transmits to the raphe nuclei via the dorsomedial hypothalamic nucleus altering serotonin levels for sleep/wake states.