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Minor histocompatibility antigens (miHags) are recognized by alloreactive cytotoxic donor T lymphocytes and trigger potent immune reactions such as graft-versus-host disease (GvHD) after major histocompatibility complex-matched transplantation. Our study focuses on tissue-specific T-cell responses to miHag-encoded peptides in GvHD target organs during the first 30 days in a murine transplant model.Complementarity determining region (CDR)3-size spectratyping was used to study T cell receptor (TCR) repertoires in recipient skin, liver, ileum, colon, spleen, and heart.GvHD occurred as early as day 14 and was proven by histology in skin, liver, ileum, and colon. The heart was histologically not affected by GvHD but showed endomyocardial “quilty lesions.” Two distinct patterns of TCR diversities could be identified. In skin, a restricted Vβ usage in combination with all Jβ segments contrasted with a complete Vβ repertoire in intestinal organs combined with a restricted Jβ usage. Interestingly, TCR repertoire in the heart was almost identical with intestinal CDR3-size patterns. Persisting clones were found in skin from day 9 to 30. In intestine and heart, identical sequences were obtained from several organs on day 14 and 21, but no persistence of CDR3 sequences could be observed.These results suggest that in the skin a limited number of persisting T cell clones maintains GvHD, whereas in the intestine, temporary expansions of different clones may fuel the process of GvHD. Strategies that eliminate tissue-specific T cells on the basis of their activational status rather than their Vβ expression but at the same time preserve a broad, overall TCR repertoire will help to increase the efficacy and safety of allogeneic stem cell transplantation.