Among the most common organ-specific autoimmune diseases are autoimmune thyreopathies. We have focused on the importance of Th1, Th2 and Th17 lymphocytes in autoimmune thyroiditis (AT). The cohort consisted of 136 treated patients in the full clinical course of AT (24 men, mean age 41.0±16.8 years and 112 women, mean age 44.6±17.6 years). The control group consisted of 17 healthy men (mean age 44.0±5.0 years). Box-Cox transformation of the data, t-tests and Pearson correlation analysis were used for statistical calculations. Lymphocyte subpopulations were determined by flow cytometry. We found statistically significant correlations between Th and Tc lymphocytes (r = -0.5605, p = 0.0000), total T and B lymphocytes (r = -0.4877, p = 0.0000), Th1 and Th17 lymphocytes (r = 0.4346, p = 0.0000), Tc and Th1 lymphocytes (r = 0.4124, p = 0.0000), IRI and Th1 lymphocytes (r = -0.4076, p = 0.0000), total T lymphocytes and NK cells (r = -0.8175, p = 0.0000), memory Th and Th1 lymphocytes (r = 0.7982, p = 0.0000), naive Th and Th1 lymphocytes (r = -0.7995, p = 0.0000), Tc lymphocytes and NK cells (r = -0.4014, p = 0.0000), Tc and total T lymphocytes (r = 0.4551, p = 0.0000), Th and total T lymphocytes (r = 0.4135, p = 0.0000). The determination of lymphocyte subpopulations is an aid in the diagnosis and treatment of autoimmune diseases, helps to clarify the clinical manifestations of the disease and can complement the interpretation of commonly determined autoantibodies. It can help determine whether the phase is destructive (Th1, Th17, Tc lymphocytes) or protective (Th2 lymphocytes, antibodies).