The spinal cord is the major conduit for nerves connecting the brain to the body. It is considered part of the central nervous system, but the nerve tracts that run through it and innervate sensory receptors, muscles, and glands belong to the peripheral nervous system, described in the introduction to PNS. If the spinal cord of an animal is severed, it will lose the ability to move and feel sensations in any body parts with nerves located below the point of severance. However, it can still carry out some reflexes and cause some simple, repetitive movements. The movements seen in a spinal animal are caused by the repeated firing of sets of neurons called pattern generators. In a normal animal, pattern generators save time by repeatedly and automatically firing to generate repetitive actions, such as walking. Pattern generators are normally controlled by nerves from the brain, but in the absence of any input, they can still cause normal patterns of rhythmic movement.

The spinal cord also mediates certain reflexes, known as spinal reflexes. One example of a spinal reflex is the movement away from a painful stimulus. For example, if I put my hand on a hot stove, I need to withdraw it as quickly as possible. To save time, the nervous system is arranged so that the pain signal does not need to travel all the way up to the brain to cause a response; the spinal cord can receive the painful input and immediately initiate the flexion reflex, causing my arm muscle to contract to withdraw my hand from the stove. An animal with a severed spinal cord will still withdraw its paw from a pinprick, even though it shows no awareness of the pain (no vocal cries or facial expressions indicating pain).

The brainstem is a subcortical structure that lies at the top of the spinal cord. The brainstem is the site of entry into the brain for ten of the twelve cranial nerves, nerves that send signals to and from parts of the head and neck. The brainstem encompasses three neural centers: the medulla, pons, and midbrain, pictured below. The medulla and the pons organize many complex and sustained reflexes. The postural reflexes help maintain posture and balance, and the vital reflexes mediate necessary internal functions such as breathing and heart rate. The midbrain controls basic movement patterns involved in feeding, grooming, and attacking. The neural centers of the midbrain also send signals to the spinal cord to control the speed of locomotion (walking or running). The midbrain and the pons work together to maintain or change patterns of sleep and arousal.

Although the brainstem is sufficient to produce a wide range of simple movements and behaviors, it cannot direct those behaviors in any meaningful way. An animal whose nervous system is severed completely just above the brainstem, eliminating any communication between the body and the rest of the brain, can still demonstrate almost all normal behaviors, including walking, running, eating, copulating, grooming, and attacking. Thus, we know that the brainstem is all that is needed to produce those behaviors. However, the animal does not direct those behaviors toward any particular goal or perform them spontaneously; it only reacts to immediate stimuli. For example, if placed on a treadmill, it will walk, but will not spontaneously walk toward an interesting object. Other, higher-up parts of the brain are necessary to produce spontaneous, goal-oriented behaviors.