BACKGROUND: Different physical exercise interventions for pain and other related symptoms largely follow non-personalized guidelines and show a high degree of variability in outcome. These interventions are considered to have different pathways toward improvement in autonomic regulation of energy metabolism. The current pilot study was conducted to assess the predictive value of individual cardiovascular (CV) activity markers at rest to predict clinical outcomes for two popular exercise-based interventions (walking and yoga) in patients with Irritable Bowel Syndrome (IBS). METHODS: Twenty-seven adult participants with IBS were randomly assigned to a 16-biweekly Iyengar yoga or walking program. They completed pre- and post-treatment assessments on IBS symptom severity, affective and somatic complaints, and various measures of resting autonomic function including blood pressure (BP), heart rate and its variability, baroreceptor sensitivity (BRS) to activations and inhibitions with gains of brady- and tachycardiac baro-responses, and BP start points for these spontaneous baroreflexes. RESULTS: Pretreatment BRS was differentially related to clinical response for the treatment groups. Specifically, a significant decrease in pain severity was found in response to yoga for those participants who had lower resting BRS to activations, but decreased pain severity was associated with higher resting BRS for those in the walking group. The effect was not related to affective symptom relief. Other CV measures showed similar associations with clinical outcomes for both groups. CONCLUSIONS: The data suggest therefore that CV based phenotypes may be useful in personalizing clinical interventions for IBS. They may also point to autonomic mechanisms that are targets for such interventions.