Methods and systems for stimulating a gastrointestinal system and for modifying a stimulation signal based on an indicator of autonomic nervous system function are described. One indicator of autonomic nervous system described is cardiac activity, including heart rate variability. Methods for selecting candidate patients for gastrointestinal stimulation therapy based on an indicator of autonomic nervous system function and methods of treating patients at risk of or suffering from gastrointestinal disorders by modifying therapy based on an indicator of autonomic function are also discussed.