The aim of this randomized controlled single-blind study is to explore whether addition of mud-pack and hot pool treatments to patient education make a significant difference in short and mild term outcomes of the patients with fibromyalgia. Seventy women with fibromyalgia syndrome were randomly assigned to either balneotherapy with mud-pack and hot pool treatments (35) or control (35) groups. After randomization, five patients from balneotherapy group and five patients from control group were dropped out from the study with different excuses. All patients had 6-h patient education programme about fibromyalgia syndrome and were given a home exercise programme. The patients in balneotherapy group had heated pool treatment at 38 °C for 20 min a day, and mud-pack treatment afterwards on back region at 45 °C. Balneotherapy was applied on weekdays for 2 weeks. All patients continued to take their medical treatment. An investigator who was blinded to the intervention assessed all the patients before and after the treatment, at the first and the third months of follow-up. Outcome measures were FIQ, BDI and both patient's and physician's global assessments. Balneotherapy group was significantly better than control group at after the treatment and at the end of the first month follow-up assessments in terms of patient's and physician's global assessment, total FIQ score, and pain intensity, fatigue, non-refreshed awaking, stiffness, anxiety and depression subscales of FIQ. No significant difference was found between the groups in terms of BDI scores. It is concluded that patient education combined with 2 weeks balneotherapy application has more beneficial effects in patients with fibromyalgia syndrome as compared to patient education alone.