What is current knowledge? Stress is an important component in the pathophysiology of Irritable Bowel Syndrome (IBS). Long term hypothalamic-pituitary-adrenal (HPA)-axis activity can be studied by measuring cortisol in hair. What is new? Low concentrations of cortisol in hair were more common in IBS patients compared to non-IBS patients. Self-reported perceived stress was higher in IBS patients compared to non-IBS patients. Our findings reveals a possible suppression of the HPA-axis activity in a considerable proportion of IBS patients.