The immunohistological findings in the thymus after bone marrow transplantation were studied in autopsy samples from 12 patients who had received allogeneic grafts as treatment for acute leukemia. The findings were compared with those in samples from normal individuals and from conventionally treated leukemic patients. The thymuses were hyperinvoluted in all grafted and nongrafted subjects. The remnants were composed of subcapsular and medullary epithelium which expressed the same phenotype as the normal thymus controls. Most samples also contained small remnants of cortical epithelium which lacked normal expression of HLA-DR antigens. The intraepithelial and stromal thymic lymphocytes were virtually all mature T cells, and no immature cortical thymocytes were seen. With the use of HLA-typing methods in 2 recipients of one-haplotype-matched grafts no donor cells could be identified in any of the thymic components. These findings provide no evidence for a functional role for the thymus in the differentiation of donor-derived precursor T cells, at least in the early period after transplantation.