The serotonin transporter (5-HTT) gene is considered to be a promising candidate for genetic involvement in some mood disorders owing to its role in the regulation of serotoninergic neurotransmission, In this study, we aimed to assess the significance of the 5-HTT gene in fibromyalgia syndrome (FS) as well as to find out whether the 5-HTT gene polymorphism is associated with this disease. Fifty-three mentally healthy fibromyalgia patients and 60 unrelated healthy volunteer controls were included in the study. Symptom Checklist-90-Revised (SCL-90-R), Beck Depression Inventory (BDI), and State and Trait Anxiety Inventory tests (STAI-I and 11) were applied to both patients and controls. A PCR analysis of 5-HTT gene polymorphism was performed. and he results of the patients with FS and healthy controls were compared. In both FS patients and healthy controls the S/S, S/L and L/L alleles of the 5-HTTLPR genotype were represented in 24.5% and 33%, 56.6% and 38.3%, and 18.9% and 28.3%. respectively. Additionally, in FS patients and healthy controls the 10/10, 10/12 and 12/12 alleles of the VNTR variant were represented in 5.9% and 11.7, 51% and 36.7%, and 43.1% and 51.7%, respectively. The 5-HTTLPR and VNTR results of the patients and controls were not significantly different (P > 0.05). We concluded that neither 5-HTT nor its polymorphism is associated with FS. Our results also address the frequencies of 5-HTT gene alleles in our population. Further studies are required to better understand the genetic basis of FS.