In neuroanatomy, habenula (diminutive of Latin habena meaning rein) originally denoted the stalk of the pineal gland (pineal habenula; pedunculus of pineal body), 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, this term refers to this separate cell mass in the caudal portion of the dorsal diencephalon, known as the epithalamus, found in all vertebrates on both sides of the third ventricle. It connects the forebrain and midbrain within the epithalamus. It is embedded in the posterior end of the stria medullaris from which it receives most of its afferent fibers. By way of the fasciculus retroflexus (habenulointerpeduncular tract) it projects to the interpeduncular nucleus and other paramedian cell groups of the midbrain tegmentum.

Although they were predominantly studied for their demonstration of asymmetrical brain development and function, in recent years many scientists have begun to examine the habenular nuclei's role in motivation and behavior as it relates to an understanding of the physiology of addiction. Functionally, the habenula is involved in nociception, sleep-wake cycles, reproductive behavioural, and mood (see section on depression below). It is one of the few areas known to influence virtually all monoaminergic systems in the brainstem, such as dopamine, norepinephrine, and serotonin.