Patients with fibromyalgia syndrome (FMS) have impaired mobility and therefore get less sunlight exposure, we postulated that they may be at increased risk of developing osteoporosis (OP). The aim of this study was to assess and compare serum vitamin D level and bone mineral density (BMD) value in patients with primary FMS (PFMS) and healthy controls. A total of 50 patients with PFMS participated in this case-control study, and 50 healthy females who were age-matched to the patients were used as the control group. Venous blood samples collected from all subjects were used to evaluate serum 25-hydroxyvitamin D3 (25-OHD). BMD was measured at the lumbar spine (L2-L4) anteroposterior, femoral neck and forearm by dual-energy X-ray absorptiometry. Patients with PFMS had significantly lower serum 25-OHD than controls (15.1 ± 6.1 and 18.8 ± 5.4 ng/ml, respectively, p = 0.0018). Apart from the BMD in the lumbar spine, which was significantly lower in the PFMS patients compared with controls (p = 0.0012), no significant difference was found in other measures of BMD. Compared to PFMS patients who had serum level of the 25-OHD >20 ng/ml, the patients with 25-OHD ≤20 ng/ml are more likely to have impaired short memory (46.4 vs. 13.6%, respectively, p = 0.0136), confusion (50 vs. 18.2%, respectively, p = 0.0199), mood disturbance (60.7 vs. 27.3%, respectively, p = 0.0185), sleep disturbance (53.6 vs. 22.7%, respectively, p = 0.0271), restless leg syndrome (57.1 vs. 27.3%, respectively, p = 0.0346) and palpitation (67.9 vs. 36.4%, respectively, p = 0.0265). Serum level of the 25-OHD is inversely correlated with visual analogue scale (VAS) of pain (p = 0.016), Beck score for depression (p = 0.020) and BMD at lumbar spine (p = 0.012). The lumbar BMD inversely correlated with VAS of pain (p = 0.013) and Beck score for depression (p = 0.016). This study confirmed high prevalence of hypovitaminosis D among in patients with PFMS. This study confirmed the concept that FMS is a risk factor for OP. Based on this, an early nutrition program rich in calcium and vitamin D, appropriate exercise protocols, and medical treatment should be considered in these patients in terms of preventing OP development.