The purpose of this study was to evaluate the relationship between temporomandibular joint pain and dysfunction and serotonin transporter (5-HTT) gene polymorphism. Forty-eight patients with temporomandibular joint pain and 111 healthy control subjects were examined. The results for the patients and control subjects were not significantly different (P > .05). The analysis of genotype distribution (homozygous for STin 2.10 genotypes of the variable-number tandem-repeat polymorphism) showed significant differences between the patients and control subjects (P = .003). ST 2.10 allele was more frequent in the patients with temporomandibular joint pain and dysfunction. In the control group, however, STin 2.12/12 genotype was significantly higher (P = .017). In the patients who were homozygous or heterozygous for variable-number tandem-repeat variants of 5-HTT STin 2.12 copies, the average scores of somatization and anger were significantly higher than those who were homozygous for STin 2.10 variant (P < .05). The patients who were homozygous for STin 2.10 genotype were also homozygous for “L” genotype (P = .019). However, this was not the condition in the control subjects. This study does not provide evidence to support the involvement of 5- HTT gene-linked polymorphic region in temporomandibular joint pain and dysfunction. Our findings indicated that only the presence of the homozygous STin 2.10 genotype of variable-number tandem-repeat is likely to play a substantial role in the genetic predisposition to temporomandibular joint pain and dysfunction and that the STin 2.12/12 genotype may have a protective role against temporomandibular joint pain and dysfunction.