Spinal cord injury (SCI) is commonly associated with devastating paralysis. However, this condition also results in a variety of autonomic dysfunctions, primarily: cardiovascular, broncho-pulmonary, urinary, gastrointestinal, sexual, and thermoregulatory. SCI and the resultant unstable autonomic control are responsible for increased mortality from cardiovascular and respiratory disease among individuals with SCI. Injury level and severity directly correlate to the severity of autonomic dysfunctions following SCI. Following high cervical SCI, parasympathetic (vagal) control will remain intact, while the spinal sympathetic circuits will lose their tonic supraspinal autonomic control. On the other hand, in individuals with injury below the 5th thoracic segment, both the sympathetic and parasympathetic control of the heart and broncho-pulmonary tree are intact. As a result of injury level, individuals with quadriplegia versus those with paraplegia will have very different cardiovascular and respiratory responses. Furthermore, similar relationships can exist between the level of SCI and function of other organs that are under autonomic control (bladder, bowel, sweat glands, etc.). It is also important to appreciate that high cervical injuries result in significant respiratory dysfunctions due to the involvement of the diaphragm and a larger portion of the accessory respiratory muscles. Early recognition and timely management of autonomic dysfunctions in individuals with SCI are crucial for the long term health outcomes in this population.