Introduction: The irritable bowel syndrome (IBS) is a complex disorder that is associated with altered gastrointestinal motility, secretion, and sensation. Serotonin directly and indirectly affects intestinal motor and secretory function and abnormalities may lead to either constipation or diarrhea. The serotonin selective reuptake transporter (SERT), terminates the actions of serotonin by removing it from the interstitial space. Polymorphisms in the promoter region of the SERT gene have effects on transcriptional activity, resulting in altered serotonin reuptake efficiency. The aim of this study was to assess the potential association between SERT polymorphism and type of intestine disorder in patients with diffuse toxic goiter and irritable bowel syndrome. Material and methods: We have investigated 38 women with diffuse toxic goiter and irritable bowel syndrome. DNA of all subjects was analysed by polymerase chain reaction based technologies for SERT polymorphism. The patients were divided into 3 groups. The first group included 12 patients with diffuse toxic goiter combined with IBS with a predominance of diarrhea, second group - 12 patients with a predominance of constipation. Third group consisted of 14 persons with thyrotoxicosis without violation of the digestive system. Results: In a first group of patients we have found all types of polymorphism: 67% homozygous LL alleles carriers gene SERT, 25% - SS-genotype, and only 1 patient (8%) was heterozygous carrier of LSvariant. Among persons of second group were 75% patients with LS-genotype, 25% had SS-variant. In the third group 79% patients had SS-genotype and 21% - LS-genotype. Conclusion: These results confirm the association between SERT gene polymorphism and diffuse toxic goiter with IBS.