Sumnlal~The graft-vs.-host reaction (GVHR) results in damage to the epithelial and lymphoid compartments of the thymus and thus in abnormal maturation and function of thymocytes in mice undergoing GVHR. In this report, the effects of GVHR on thymic T cell receptor (TCR) expression and usage have been investigated. GVHK was induced in unirradiated F1 hybrid mice by the intravenous transfer of parental lymphoid cells. Expression of the CD3/TCR complex on thymocyte subsets defined by CD4 and CD8 was studied by three-color flow cytometry. The level of CD3/TCK was decreased on CD4+CD8 -, but not CD4-CD8 § mature thymocytes. The lack of upregulation of CD3/TCR on CD4 single-positive thymocytes, but not on their CD8 + counterparts, suggested an abnormality of class II major histocompatibility complex (MHC) expression in the thymuses of mice undergoing GVHK. Immunofluorescence staining of thymic frozen sections revealed that MHC class II expression was dramatically decreased in GVH-reactive mice. GVHK-induced changes in positive and negative selection were evaluated by determining the incidence of specific VB TCK segment usage in the thymus. In normal mice, thymocyte usage of any given V3 segment was highly consistent between individuals of the same strain and age; however, a marked divergence in the incidence of TCK V36 hi and VB8 hi cells between GVH-reactive littermate mice was observed, suggesting that thymic positive selection had become disregulated in these animals. Furthermore, negative selection was defective; the incidence of phenotypically self-reactive VB6 hi T cells was significantly greater in the thymuses of GVHreactive mice bearing the endogenous superantigen Mls-P than in untreated controls. Thus, mice undergoing GVHK showed defective TCK upregulation on CD4+CD8 -thymocytes and changes in TCK usage reflecting aberrant thymic selection, in conjunction with decreased expression of MHC class II. Most abnormalities of TCR expression and usage on CD4 + thymocytes observed in GVH-reactive mice were analogous to those of class II knockout mice.