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The cerebellum lies dorsal to the midbrain and pons, and rostral to the medulla oblongata. It is not considered to be part of the brain stem, but it is connected to the midbrain, pons, and rostral medulla oblongata by the bilateral superior, middle, and inferior peduncles respectively. The cerebellum is separated superiorly from the cerebrum by the tentorium cerebelli.

The ventral surface of the brain stem faces the bony wall of the basiocciput. Inferiorly, the caudal portion of the medulla oblongata passes through the foramen magnum, and continues as the spinal cord.