The specificity with which CD4+ T cells recognize self peptides in vivo was examined in transgenic mice that express an influenza virus PR8 hemagglutinin (HA) polypeptide in many tissues, including the thymus (HA Tg mice). HA Tg and non-Tg mice were analyzed for their T cell responses to the major PR8 HA I-E(d)-restricted CD4+ T cell determinant S1. Negative selection eliminated S1-specific T cells from HA Tg mice. Nevertheless, HA Tg mice retained the ability to mount a T cell response to a closely related analog of the S1 determinant [S1(K113)], and some S1(K113)-specific TCRs displayed a partial reactivity with S1 as indicated by their ability to transmit signals for IL-3 but not IL-2 secretion in response to the neo-self peptide. Moreover, the neo-self S1 peptide antagonized the ability of these TCRs to signal IL-2 secretion in response to the foreign S1(K113) determinant. Thus, TCRs that exhibit a partial reactivity with a self peptide are present in the peripheral T cell repertoire and can be activated by a virus containing an analog of the self peptide. These findings provide a model for the induction of autoimmunity by viruses that are close homologs of self peptides, and suggest a way in which TCRs could react with self peptides during positive selection of developing thymocytes.