Introduction: Hashimoto thyroiditis (HT) is a chronic autoimmune inflammation of the thyroid gland with a complex genetic background and of unknown etiology. Immunopathogenesis of HT is partially mediated by autoreactive T lymphocytes with altered development functional features, potentially as a consequence of the increased expression of TBX21, EOMES and RUNX3 genes. Allelic forms of the rs4648889, rs11129295 and rs4794067 polymorphisms quantitatively affect expression of RUNX3, EOMES and TBX21 genes, but their role in the incidence of HT has not been investigated. Research objectives: Genotyping of the rs4648889, rs11129295 and rs4794067 polymorphisms and analysis of the connection between allelic an genotypic forms with expression of RUNX3, EOMES and TBX21 genes in peripheral T lymphocytes in HT patients and the controls. Materials and methods: The research included a collection of archive DNA samples isolated from the peripheral blood of adult, unrelated, HT patients and healthy individuals with previously measured level of TBX21, EOMES and RUNX3 genes expression in peripheral T lymphocytes. From the previously defined patients population, the DNA samples were chosen for genotyping of eQTL polymorphisms and the groups of HT patients and controls were defined for genotyping of rs4794067 (HT/CTRL= 30/10), rs11129295 (HT/CTRL=28/9) and rs4648889 polymorphisms (HT/CTRL= 33/10). Results: Compared to controls (CTRL), the HT patients show a significantly increased mRNA expression of TBX21 and RUNX3 genes. A quantitative effect of genotype forms of rs4794067 and rs 11129295 polymorphisms on the expression level of TBX21 and EOMES genes has not been observed. Conversely, the „AG“ genotype patients of rs 4648889 polymorphism show a significantly decreased expression of RUNX3 compared to the homozygous genotypes „AA“ and „GG“. Conclusion: For a precise analysis of quantitative effects of the specified polymorphisms on HT development, a higher number of patients have to be included in the research.