The paper gives the results of morphological and immunohistochemical studies of the thymus in congenital hypoxia induced by the intrauterine development of heart diseases. The morphological changes in the thymic structure have been found to depend on the complicacy of the heart defect determining the degree of hypoxia. There are significant thymic structural changes manifesting themselves as disorders of the epithelial stroma. Its destruction areas exhibit activated fibroblastic differon that positively responds to vimentin and CD34. Increased resistance of lymphocytes to apoptosis has been ascertained and their proliferative properties determined. There is a progressive accumulation of the antiapoptotic protein Bcl-2 in the cytoplasm of thymocytes in the cortex of a thymic lobe and a decrease in Ki-67 expression in the lymphocytes in the thymic lobes, especially in cases of severe heart defects.