Histological and immunohistochemical studies of the pineal and pituitary glands of the Greater Cane Rat (GCR) were carried out using four apparently healthy young adult males obtained from Lagos, South West Nigeria. Their brains were harvested after perfusion, the pineal and pituitary glands were carefully dissected. Tissue sections were prepared and stained using haematoxylin and eosin (H&E), Cresyl violet, glial fibrillary acidic protein (GFAP), ionized calcium-binding adapter molecule 1 (IBA1), neuronal nuclei (NeuN) and collagen type 1 antibodies for histological and immunohistochemical analysis. Grossly, the pineal gland of GCR is a pine-cone shaped midline structure. H&E staining showed type I (light) and type II (dark) pinealocytes, arranged in cord and cluster of cells within the pineal parenchyma. Immunohistochemically, the astrocytic-like (GFAP+); microglial cells (IBA1+); neurons (NeuN+) and collagen fibres were localized in the pineal gland. The GCR pituitary gland is a disc-shaped organ located in the ventral part of the brain within the sella turcica. Routine staining delineated the neurohypophysis, intermediate lobe, adenohypophysis and hypophyseal cleft. Histological examination revealed fibrous and protoplasmic pituicytes which were observed among the non-myelinated fibres and herring bodies in the neurohypophysis. The acidophils, basophils and chromophobes appeared in cords and clusters in adenohypophysis, and the melanotrophs in the intermediate lobe. Immunohistochemical studies highlighted GFAP+ pituicytes as the resident astrocytes of neurohypophysis and the presence of collagen fibres in neurohypophysis. In conclusion, the histological and immunohistochemical features of pineal and pituitary glands in the GCR are similar to other rodents and mammals, though some peculiarities exist.