Objectives: Imbalances in effector T cell functioning have been associated with a number of autoimmune diseases, including Hashimoto's thyroiditis (HT). Differentiation of effector T helper (Th) 1. Th2, Th17 and regulatory T cell (Treg) lymphocytes is regulated by transcription factors, including Th1-specific T box (T-bet). GATA binding protein-3 (GATA,), retinoid-related orphan receptor (ROR)-a and forkhead box P3 (FOXP3). This study aimed to investigate Th1/Th2. Th1/Treg. Th2/Treg and Th17/Treg balances at the level of these transcription factors. Methods: This study took place between October 2015 and August 2016. Peripheral blood mononuclear cells were collected from a control group of 40 healthy women recruited from the Zahedan University of Medical Sciences, Zahedan, Iran, and a patient group of 40 women with HT referred to the Hazrat Ali Asghar Hospital. Zahedan. Total ribonucleic acid extraction was performed and the gene expression of transcription factors was quantitated using a real-time polymerase chain reaction technique. Results: Expression of T-bet and GATA, was significantly elevated, while FOXP3 expression was significantly diminished among HT patients in comparison with the controls (P=0.03, 0.01 and 0.05, respectively). Expression of RORa was higher among HT patients, although this difference was not significant (P = 0.15). Expression of T-bet/FOXP3, GATA/FOXP3 and ROR/FOXP3 ratios were increased among HT patients in comparison with the controls (P <0.02, <0.01 and <0.01, respectively). Conclusion: These results indicate that HT patients have imbalances in Th1/Treg. Th2/Treg and Th17/Treg lymphocytes at the level of the transcription factors, deviating towards Th1. Th2 and Th17 cells. Correction of these imbalances may therefore be therapeutic.