Background <p>Fibromyalgia Syndrome (FMS) predominantly affects middle-aged women, characterized by musculoskeletal pain, fatigue, and cognitive issues. Choline, an endogenous molecule, may influence FMS due to its analgesic and anti-inflammatory properties. This study compared choline, leptin, and interleukin-6 (IL-6) levels in FMS patients and controls and examining their association with pain severity.</p> Methods <p>Volunteers with FMS were clinically diagnosed at a Physical Medicine and Rehabilitation Department. The control group included pain-free volunteers. Pain severity was gauged using a numeric scale, dietary choline intake through a questionnaire. Serum choline, leptin and (interleukin)IL-6 levels were measured from fasting blood samples of volunteers with enzyme-linked immunosorbent assays (ELISA).</p> Results <p>All FMS patients (<i>n</i> = 38) and healthy volunteers (<i>n</i> = 38) were female. Pain score in patients with FMS was 7.6 ± 0.2. Dietary choline intake was lower in patients with FMS than the controls (<i>p</i> = 0.036). Serum choline and leptin levels were lower in the FMS group compared to control (<i>p</i> = 0.03). Serum IL-6 levels were higher in the FMS group than in the control (<i>p</i> &lt; 0.001). There was weak positive correlation between IL-6 levels and pain scores and there were no correlation between leptin levels and pain scores in FMS.</p> Conclusions <p>This research highlights FMS's complex nature, involving neurochemical, immunological, and nutritional factors. It suggests the significance of choline's anti-inflammatory effect, leptin's metabolic function, and IL-6's role in FMS pathology. The results suggest that reduced dietary choline might influence serum choline, leptin, and IL-6 levels, potentially impacting FMS-related pain. This points to the potential of supplementary choline intake in FMS management.</p> Trial registration <p>Not applicable (Non-interventional study).</p>