Irradiation of mice with energy-fast carbon ions 4.0 in dose impairs histological structure of thymus on the first day after the challenge. Non differentiated cell forms (blasts and large lymphocytes) and middle lymphocytes were most sensitive to the irradiation. As a result mitotic activity decrease was noted. Reparative process in thymus begins on d 22 after irradiation with carbon ions when stem cells obviously accumulate. At the same time mitotic activity intensifies. Although at distant terms T cells differentiation and formation are inhibited which is reflected in significantly reduced number small lymphocytes in thymus cortex and medulla on d 60 of postirradiation period as compared to that in control.