Chronic pain is often equated with chronic stress yet the relationship between chronic pain and hypothalamic-pituitary-adrenal (HPA) axis activity is poorly understood. The objective of this study was to examine diurnal functioning of the HPA axis in patients with clinically defined non-inflammatory chronic pain syndrome (CPS) compared to controls. The sample consisted of 37 adults with CPS and 47 healthy controls. All participants provided saliva samples at awakening, 12:00, 18:00 and 21:00 h on two consecutive days, as well as completing self-report questionnaires relating to anxiety and depression. The CPS group had a significantly lower overall mean diurnal salivary cortisol concentration compared to the control group (p < 0.01) but no significant differences were found between the two groups for repeated cortisol sampling across the day. However, a three-way interaction of time of day by patient status by sex was found (p < 0.032), with lower cortisol concentration in male patients compared to female patients in the afternoon period. No significant group effect was found for the rate of decline in the circadian rise in cortisol concentration. These data demonstrate that CPS is associated with a degree of hypocortisolemia, particularly in male patients. The altered dynamics of cortisol secretion in CPS in relation to the onset and duration of pain in patients remains to be determined.