Despite the extensive impact of autonomic function on the gastrointestinal system, there is little understanding of the mechanisms by which specific autonomic abnormalities translate into particular gastrointestinal complaints. Three logical alternatives include: (1) the underlying disorder affects the autonomic and gastrointestinal systems independently; (2) autonomic dysfunction alters gastrointestinal processing directly; (3) gastrointestinal manifestations arise as a delayed, indirect consequence of autonomic dysfunction. The major gastrointestinal manifestations of dysautonomia include esophageal dysmotility such as achalasia, gastroparesis, and small bowel bacterial overgrowth in the upper tract. Lower tract disorders include diarrhea, fecal incontinence, and constipation. Sorting through the varied causes of these disorders requires a careful history and examination in each patient. Supportive diagnostic studies may include radionuclide imaging, motility examination, and electrogastrography. Autonomic studies can (1) distinguish a purely enteric from a more generalized dysautonomia; (2) provide surrogate information about motility; (3) differentiate primary (e.g., multiple system atrophy) from secondary (e.g., irritable bowel syndrome) dysautonomias as the etiology of gastrointestinal symptoms. Several new strategies are available for the treatment of gastroparesis, constipation, irritable bowel, and sphincteric incontinence.