The self-restricted T cell repertoire exhibits a high frequency of alloreactivity. Because these alloreactive T cells are derived from the pool of cells selected on several different self MHC alleles, it is unknown how development of the alloantigenic repertoire is influenced by homology between a self MHC allele and an alloantigen. To address this, we used the 2C transgenic TCR that is selected by Kb, is alloreactive for Ld, and cross-reacts with Lq. Lq is highly homologous to Ld and binds several of the same peptide ligands, including p2Ca, the peptide recognized by 2C. We find that Ld/p2Ca is a high avidity agonist ligand, whereas Lq/p2Ca is a low avidity agonist ligand for 2C T cells. When mice transgenic for the 2C TCR are bred to Lq-expressing mice, 2C+ T cells develop; however, they express lower levels of either the 2C TCR or CD8 and require a higher Ld/p2Ca ligand density to be activated than 2C+ T cells selected by Kb. Furthermore, the 2C T cells selected in the presence of Lq fail to detect Lq/p2Ca complexes even at high ligand density. Thus, despite possessing the identical TCR, there is a functional avidity difference between 2C+ T cells selected in the presence of Lq vs Kb. These data provide evidence that homology between the selecting ligand and an alloantigen can influence the avidity of the T cell repertoire for the alloantigen, and suggest that thymic selection can fine tune T cell avidity independent of intrinsic TCR affinity.