It has been recently suggested that the expression of two different isofoms of tyrosine phosphatase antigen (CD45RA and CD45RO) could differentiate T cells into autoreactive and immunoregulatory subsets, which play a crucial role in the autoimmunity process. The aim of the present study was to evaluate the differences between the distribution of memory, naive and recently activated T cells (co-expressing both CD45RA and CD45RO antigens) in the peripheral blood of patients with newly diagnosed Graves' disease and insulin-dependent diabetes mellitus in comparison to healthy controls. The study was carried out in 3 groups: 18 patients with Graves' disease, 16 subjects with a recent onset of type 1 diabetes mellitus and 16 healthy, age and sex matched volunteers. At the onset of both autoimmune diseases the percentage of naive CD+ cells were lower than in the control group and in patients with Graves' disease treated with methimazole. The analysis of CD8+ lymphocyte subsets in the peripheral blood revealed higher levels of CD8+CD45RO+ cells in the newly diagnosed Graves' disease in comparison to the controls, and significant decline in the percentage of memory CD8+ and CD8+CD45RA+CD45RO+ lymphocytes after thyreostatic treatment. The number of CD4+ T lymphocytes co-expressing CD45RA and CD45RO antigens were statistically higher in the patients with recently diagnosed insulin-dependent diabetes mellitus. The abnormal distribution of naive, memory and "transient" T cell subsets in the peripheral blood at the onset of Graves' disease and diabetes type 1 suggest their role in the development of autoimmunity. The significant alterations of lymphocyte T subsets in the peripheral blood of patients with Grave's disease after thyreostatic therapy in comparison to the newly diagnosed subjects supports the immunomodulatory effect of methimazol treatment.