The thymus is an important organ for producing T cells. Thymic structures consist of thymic epithelial cells among which thymocytes proliferate and maturate. The structural and functional recovery of the rat thymus after irradiation was studied morphologically and by the message expression changes of several cytokines. In this manuscript we tried to describe further details of rat thymic epithelial cells in respect to therir electron microscopic features as well as their function to interact with thymocytes. Then the mechanisms responsible for the regeneration of the thymus after irradiation were considered. Not only the reproliferation of the thymocytes but also the regeneration of the vasculatures and thymic epithelial cells are considered important for thymus regeneration. Cytokine message changes were shown to be seriously involved for the degree of recovery of the thymus tissue after irradiation.