Background and Objective: Obstructive sleep apnea syndrome (OSAS) is a common condition characterized by repetitive pharyngeal collapse during sleep and daytime sleepiness. There is genetic predisposition to sleep disorders. Serotonin is involved in the regulation of sleep. The synaptic 5-hydroxytryptamine (HT) is inactivated by presynaptic reuptake, which is mediated by the serotonin transporter. Blockage of the serotonin transporter leads to increased extracellular 5-HT. Polymorphism of the serotonin transporter gene (STG) leads to alterations in serotonin level and may be important in OSAS. In this study, we aimed to assess the role of STG polymorphism in OSAS. Methods: Twenty-seven OSAS patients and 162 healthy volunteers were involved in the study. STG polymorphism was investigated using leukocytes obtained from peripheral blood. Results: There was no difference between the genotypes and allele frequencies of the patients and controls regarding VNTR and HTTLPR polymorphisms (P >.05). The VNTR and HTTLPR variants and the frequencies of 12/12, 12/10, L, and S alleles were not significantly different between male and female control subjects (P >.05). The 12/12 and SS genotypes were over-represented in the female patients, whereas 12/10 and LL genotypes were over-represented in the male patients (P <.05). The genotypes 12 to 12 were over-represented in the male controls, whereas the genotypes 12 to 10 and US were over-represented in the male patients (P <.05). The alleles 10 and L were more frequent in the male patients than male controls (P <.05). The genotypes of female patients and female controls were not significantly different (P >.05). The allele 10 and L were less frequent in the female patients than female controls with Fisher's exact testing (P <.05). There was no relation between genotypes and clinical data of the patients (P >.05). Conclusion: STG polymorphism appears to be associated with the occurrence of OSAS, especially in male patients. Absence of association of between genetic variants and polysomnography findings may suggest that some mechanisms other than STG polymorphism are involved in OSAS pathophysiology. Our results need confirmation in a larger group of patients with OSAS.