Background Irritable bowel syndrome (IBS) is conceptualized as a syndrome of enhanced central stress circuit responsiveness, likely associated with altered adrenergic and autonomic responses. Aims (1) To determine if baseline autonomic nervous system (ANS) differences exist in IBS versus control subjects; (2) to determine group differences in ANS response to yohimbine (YOH) and clonidine (CLO); and (3) to determine group differences in the effects of YOH and CLO on affective states. Methods IBS and control subjects were enrolled. ANS and affective measures were taken before and after drug ingestion. ANS was measured by HRV (high frequency, HF, indicating cardiovagal and low/high frequency ratio, LF/HF, indicating sympathetic) and systolic BP. Affective ratings were made with the Stress Symptom Rating Questionnaire. Results Mean baseline HF was lower in IBS versus controls (34.29 nu vs 62.88 nu, p =.013). Mean baseline LF/HF was higher in IBS versus controls (2.59 vs 0.91, p =.057). No significant HRV changes were seen in response to CLO or YOH in either group. YOH significantly increased BP (p =.01) and CLO significantly reduced BP (p =.02) in pooled subjects; no group difference in BP was seen. No group differences in affective ratings were seen. In combined groups, YOH increased anxiety (p =.05) and CLO led to increased fatigue (p = 0.01) with decreased arousal (p =.02). Conclusion These findings confirm that there is greater baseline sympathetic and lower parasympathetic activity in IBS patients compared with controls. A larger sample of patients is likely needed to elucidate group differences in drug responses.