The epiphysis or pineal gland is a small, darkly pigmented outgrowth from the dorsal aspect of the brain at the caudal end of the roof of the third ventricle and directly before the rostral colliculi (see Fig. 8.22/11).

In certain species the epiphysis is related to a large outpouching (epiphyseal recess) of the pia-ependyma that roofs the ventricle. It is concealed between the cerebral hemispheres and cerebellum in the intact brain.

The epiphysis is solid but is not always homogeneous because foci of calcification ("brain sand") often develop with advancing age. It produces melatonin, an indolamine derived from serotonin, which has an antigonadotropic circadian effect. Tumors that destroy the secretory tissue have been noted to be frequently associated with precocious puberty.

The melatonin secretion by the pineal gland is controlled through a polysynaptic pathway by the endogenous circadian clock located in the hypothalamic suprachiasmatic nucleus (SCN). The autonomic innervation of the pineal gland runs via the superior cervical ganglion. Melatonin is secreted as a sleeping hormone during the night and acts on many brain areas, including the SCN and the pituitary. The brain knows that it is day from the enhanced activity of the SCN and knows that it is night from the secretion of melatonin. The action of melatonin on the pars tuberalis is important for seasonal hormonal fluctuations. Fine-tuning of the biological clock in the SCN can be achieved by gradual changes in daylight, which regulate both long-term (seasonal) and short-term (diurnal) variation in gonadal activity.