The science bit The bowel is controlled mainly by nerves leaving the spinal cord at level of T6-T12 (lower thoracic vertebrae. These nerves control the movement of abdominal muscles. The lower end of the bowel is controlled by nerves leaving the spinal cord lower down at level SS (sacral vertebrae. Some automatic (autonomic) control occurs within the bowel itself this is the part that brings the urge to use the toilet when stressed or frightened. How the bowel works after SCI After a spinal cord injury, the messages sent by the nerves located in your bowel are notable to reach your brain as before. This means you will not get the message that tells you when your bowel is full. You may also lose control of the muscle at the opening from your back passage (sphincter. Your degree of loss will depend upon your level of injury and the extent (completeness) of your spinal damage.