Autonomic nervous system function was assessed in women with and without irritable bowel syndrome using frequency domain measures of heart rate variability. Women were interviewed and placed into the irritable bowel syndrome (N = 25) group based on history of diagnosis and self-report of current gastrointestinal symptoms. Women in the control group denied a history of chronic gastrointestinal symptoms (N = 15). Women were followed for one menstrual cycle with a symptom diary, and during mid-luteal phase they wore a Holter 24-hr electrocardiograph monitor. Women with irritable bowel syndrome demonstrated significantly lower vagal tone as measured by the high frequency spectrum relative to control women. In addition, women with irritable bowel syndrome had a flattened 24-hr pattern of heart rate variability, with significantly lower levels of vagal tone during sleep. These results suggest that systemic sympathovagal balance may be shifted in a subset of women with irritable bowel syndrome.