Introduction: Hashimoto's thyroiditis (HT) is a chronic autoimmune thyroid disease developing under the influence of susceptible genetic and environmental factors. The disease is characterised by the presence of autoreactive immune cells and antibodies directed against the thyroid tissue antigens, which mediate thyroid cell destruction throughcytokine injury and apoptosis. CD8+ cytotoxic lymphocytes comprise a significant proportion of the lymphocytic thyroid infiltrate in HT patients. Their differentiation and development are regulated by a number of transcription factors such as PLZF, RUNX3, RORC and FOXO1. Study aim: To examine transcriptional profiles of PLZF, RUNX3, RORC and FOXO1 genes, and determine their association with the thyroid volume, TSH and FT4 hormone levels, anti-TPO antibodies, and the dosage of hormone replacement therapy. Material and methods: Peripheral blood was collected from 11 healthy controls and 35 HT subjects. cDNA was synthesized with the use of commercial PrimeScript First Strand cDNA Synthesis Kit, whereasquantitative analysis of mRNA expression i real time PCR instrument QuantStudio 5, was performed with a set of predisigned TaqMan expression assays. Results: Compared to the control subjects, patients with HT showed significantly increased levels of PLZF, RUNX3 and RORC mRNA expression. Moreover, the increased level of PLZF gene expression positively correlatedwith the increment of hormone replacement dose in treated hypothyroid HT patients (n = 12), and the RORC mRNA levels were associated with the increase ofthe serum TSH in untreated HT examinees (n = 23). RUNX3 transcript abundance increased with age (n = 46). Conclusion: Expression profiles of PLZF, RORC and RUNX3 genes in peripheral T lymphocytes of HT patients differ from the ones in healthy control subjects, and changes in their expression are associated with the progression of HT disease, hypothyroidism and the dosage of hormone replacement therapy.