Effects of balneotherapy on Primary Fibromyalgia Syndrome (FMS) have been studied well, except for its effect on the respiratory symptoms of FMS. In this study we allocated 56 patients with FMS into three groups who matched according to age, gender and duration of illness. All three groups received the same three physical therapy modalities (PTM): transcutaneous electrical nerve stimulation (TENS), ultrasound (US) and infrared (IR). The first group received PTM plus balneotherapy (PTM+BT), the second group received PTM alone (PTM), whilst the third group received PTM plus hydrotherapy (PTM+HT). All groups were treated for three weeks and in the same season. All patients were assessed at four time points: (a) at baseline, (b) on the 7th day of therapy, (c) at the end of therapy (after 3 weeks) and (d) at 6 months after the end of therapy. The effectiveness of treatments in all groups were evaluated in three main categories (pain, depressive and respiratory symptoms). Tender point count, total algometric measurements and pain with visual analog scale for pain; Beck Depression Inventory (BDI) and Hamilton Depression Rating Scale (HDRS) for depression; dyspnea scale, and spirometric measurements for respiratory symptoms; plus quality of life with visual analog scale as a general measurement of effectiveness were taken at all four assessment time points. Both at the end of therapy and at the 6 months follow up significant improvements in dyspnea scale, and spirometric measurements, as well as in other measured parameters were observed in group PTM+BT. All groups achieved significant improvements in BDI and HDRS but scores of PTM and PTM+HT groups had overturned at 6 months follow up. Except second group which receieved PTM alone, pain evaluation assessments were improved at 6 month follow up in PTM+HT and PTM+BT groups. But PTM+BT group had more significant improvements at the end of therapy. PTM group had no significant change for dyspnea scale and spirometric measurements. PTM combined BT and HT groups achieved significant improvements at the end of therapies for dyspnea scale and spirometric measurements, but only PTM+BT group had significant improvements for dyspnea scale and spirometric measurements at six month follow up. The group of PTM+BT was significantly better than other groups. Our results suggest that supplementation of PTM with balneotherapy is effective on the respiratory and other symptoms of FMS and these effects were better than other protocols at 6 month follow up.