The pineal gland is about 8 mm in diameter, encased in a tightly adherent pia mater, divided into a number of connective tissues wrapped lobes. Small blood vessels may be visible in the septate spaces between the lobes. The pineal gland is largely composed of two cell types, better distinguished at higher magnifications. Roughly 95% of the pineal gland consists of pinealocytes, the cells that produce the hormone melatonin which works with the hypothalamus to regulate sleep wake cycles. Pinealocytes are arranged in small clusters or rosettes. They can be identified by their large, round, pale staining nuclei, surrounded by wide rims of light staining cytoplasm. In some preparations it may be possible to see long cytoplasmic processes extending from the pinealocytes into the septae.

Closely associated with the pinealocytes are supportive astrocytes with smaller darker nuclei and long cytoplasmic projections.