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Abstract Aims Recent genetic studies have linked serotonin-related genetic polymorphisms with diverse disorders characterized by functional somatic symptoms, including chronic fatigue syndrome, irritable bowel syndrome, and premenstrual dysphoric disorder. Methods We investigated three serotonin-related genetic polymorphisms by screening genomic DNA of 36 temporomandibular disorder (TMD) patients. Results A significant increase of longer alleles (l and xl) was found in the TMD patients compared to the controls both by the genotype-wise and the allele-wise analyses (both p < 0.01 by χ2 test and Fisher's exact test). Conclusion Genetic factors that involve the serotonergic system may play a role in the pathogenesis of TMD.