We have studied the structure and diversity of TCR alpha-chain genes used by graft-infiltrating lymphocytes (GIL) in the ACI-to-LEW rat cardiac allograft model. We previously reported the structure of 16 different V alpha and 17 different J alpha genes isolated in two different cDNA libraries established from LEW thymocytes and GIL. In this report, we obtained new sequence information for 17 additional V alpha and J alpha genes from the GIL cDNA library. This study completes our characterization of 33 different V alpha and 23 different J alpha genes in rats. The V alpha genes are classified into 14 different families. Nucleotide sequence comparison with mouse alpha genes revealed the existence of mouse homologues for all the J alpha and 32 of the 33 V alpha genes. One of the rat V alpha genes seemed to have no known mouse counterpart and is classified here as a V alpha 24 gene family. The definition of rat TCR alpha-chain genes derived from these studies should facilitate a better understanding of the T cell role in pathologic conditions including autoimmune diseases and graft rejection. As for the TCR alpha-chain repertoire usage in allograft rejection, we completed the characterization of 36 productively rearranged TCR alpha-chain cDNA clones from the GIL cDNA library and found 31 different V alpha and 23 different J alpha genes among these clones. Unlike the TCR beta-chain that uses a limited repertoire, the alpha-chain repertoire usage seems to be relatively more diverse in this allograft model. These results suggest that the interaction of beta-chain with allogeneic MHC-encoded determinants may dictate the T cell reaction to the heart allograft in this model.