Habenula originally denoted the stalk of the pineal gland, but gradually came to refer to a neighboring group of nerve cells with which the pineal gland was believed to be associated, the habenular nucleus. The habenular nucleus is a set of well-conserved structures in all vertebrate animals.
Currently, the Terminologia Anatomica term refers exclusively to this separate cell mass in the caudal and dorsal aspect of the dorsal thalamus, embedded in the posterior end of the medullary stria from which it receives most of its afferent fibers. By way of the fasciculus retroflexus it projects to the interpeduncular nucleus and other paramedian cell groups of the midbrain tegmentum.
The habenula receives input from the brain via the stria medullaris thalami and outputs to many midbrain areas involved in releasing neurotransmitters, such as dopamine, norepinephrine, and serotonin.