The morphology of the deep pineal gland of the Sprague Dawley rat was investigated by serial block face scanning electron microscopy. Cells were three-dimensionally (3-D) reconstructed using the software Fiji TrackEM. The deep pineal gland consisted of 2-5 layers of electron-lucent pinealocytes, with a euchromatic nucleus, endowed with one or two processes. Laterally, the deep pineal merged with the habenula and the stria medullaris thalami, via an intermediate area containing cells with more electron-dense cytoplasm and an indented nucleus with heterochromatin. Neither nerve terminals nor capillaries were observed in the deep pineal itself but present in the intermediate parts of the gland. The deep pineal was in contact with the third ventricle via the pineal and suprahabenular recesses. The ependymal lining in these recesses was an epithelium connected by tight junctions between their lateral cell membranes. Several intraventricular nerve terminals were in contact with the ependyma. 3-D reconstructions showed the ependymal cells endowed with long slender process penetrating the underlying pineal parenchyma. Few "tanocyte-like" ependymal cells, endowed with a process, reaching the subarachnoid space on the inferior surface of the deep pineal were observed. In addition, pinealocyte and astrocyte processes, often connected by gap junctions, bordered the inferior surface. In summary, the rat deep pineal gland is a neuroendocrine structure connected to the habenula. We here report specialized ependymal cells that might transmit signals from the cerebrospinal fluid to the deep pineal parenchyma and a "trans-pineal tanocyte-like cell" that connects the ventricular system with the subarachnoid space.