Objective: Mechanisms of sleep disorders in fibromyalgia (FM) patients, such as insomnia, early morning awakenings and poor quality sleep, have not yet been proven and no consistent and effective treatment is yet available. The aim of this study was to investigate the pineal gland volume and the relationship between total fibre count, total fibre volume and total fibre length of the spinoreticular tract involved in regulation of sleep and wakefulness in terms of the mechanism of sleep disturbance. Methods: This study included only female cases, 31 with fibromyalgia and 31 controls. Pittsburgh Sleep Quality Index was used to assess sleep quality. Tractography of targeted pathway from brain diffusion MR images was calculated in Diffusion Studio Imaging (DSI) Studio programme and the volume of the pineal gland was calculated in ITK-SNAP programme. Results: The mean volume of the pineal gland was higher in control group (218.84 ± 64.45 mm³) than in fibromyalgia group (174.77 ± 48.65 mm³), which was statistically significant (p = 0.004). However, there was no statistically significant difference between two groups in total spinoreticular tract (TSRT), total volume (TSRTV), TSRT fractional anisotropy, TSRT mean diffusion, TSRT axial diffusion and TSRT radial diffusion of spinoreticular tract, which is involved in the regulation of sleep and wakefulness (p > 0.05). Conclusion: In conclusion, it is thought that the endocrine system may be more related to sleep disturbance in individuals with FM than central nervous system. Therefore, we believe that it may be more appropriate to work on the endocrine system rather than neural system in the treatment of sleep disturbance in patients with FM.