To investigated serum cortisol and serum dehydroepiandrosterone-sulphate (DHEA-S) levels between fibromyalgia (FMS) patients and a control group, and the effect of balneotherapy (BT) on these hormones.  
Seventy-two patients with FMS and 39 healthy volunteers were included in the study. This prospective and cross-sectional study was carried out in the Medical Faculty, Physical Medicine and Rehabilitation Clinic, Cumhuriyet University, Cumhuriyet, Turkey between June 2012 and June 2013. Patients were divided into 2 groups. There were 40 patients in the first group, consisting of BT and physical therapy (PT) administered patients. There were 32 FMS patients in the second group who were only administered PT. Thirty-nine healthy volunteers were enrolled as a control group.  
Cortisol was observed to be lower in FMS patients compared with the controls  (10.10±4.08 µg/dL and 11.78±3.6 µg/dL; p=0.033). Serum DHEA-S level was observed to be lower in FMS patients compared with the controls (89.93±53.96 µg/dL and 143.15±107.92 µg/dL; p=0.015). Average serum cortisol levels of patients receiving BT were determined to be 9.95±3.20 µg/dL before treatment and 9.06±3.77µg/dL after treatment; while average serum DHEA-S levels were 77.60±48.05 µg/dL before treatment, and 76.84±48.71 µg/dL after treatment. No significant changes were determined in serum cortisol and DHEA-S levels when measured again after BT and PT.  
Low levels of serum cortisol and DHEA-S were suggested to be associated with the physiopathology of FMS.