Investigations were carried out on 28 male rats Vistar line 5-6 months of age. EDM was designed by intraperitoneal injection of streptozotocyn (SIGMA, USA) at dose 50 mg/kg one time. Method of double immunofluorescence with usage of rat monoclonal anti-AIRE, anti-CD4 and rat anticytokeratin antibodies was used for revelation of AIRE. Structure of a thymus was analyzed with the help of software VIDAS. All statistical analyses were performed using EXCEL MS Office 2010 (Microsoft Corp., USA), STATISTICA 6.0 (Stat-Soft, 2001) software. Results are expressed as mean values +/- SEM. Differences were considered statistically significant if the p value was <0.05. Conclusions. In summary, although the effects of AIRE on central tolerance are well established, the cellular and molecular mechanisms are still unclear. Along with the better-understood effects on TSA expression, AIRE can also alter the differentiation program of mTECs, regulate the expression of thymic chemokines, contribute to specific Treg induction, and induce mTEC apoptosis. This novel knowledge of normal and pathologic functions of the thymus constitutes a solid basis for the development of a novel type of tolerogenic/negative self-vaccination against type 1 diabetes (T1D).