Transgenic (Tg) mice expressing the influenza virus PR8 hemagglutinin (PR8 HA) were infected with PR8 virus and analyzed for their ability to generate T cell responses to individual MHC class II-restricted T cell determinants from the HA. HAmemb and HAtrunc mice each express HA transgene mRNA in many tissues (including the thymus), but differ in the form and amount of the HA that is expressed: HAmemb mice express the entire viral HA as a membrane-bound neo-self antigen, whereas HAtrunc mice express lower levels of a truncated HA polypeptide. HAmemb mice were found to mediate efficient negative selection of autoreactive T cells directed to the major I-Ed-restricted and I-Ad-restricted determinants from the HA (designated S1 and S2 respectively). S1-specific T cell responses were similarly undetectable in PR8-infected HAtrunc mice. However, S2-specific T cells were only partially eliminated in HAtrunc mice; indeed, even though their frequency was reduced relative to non-Tg mice, S2-specific T cells still constituted a sizable population in PR8-infected HAtrunc mice. Moreover, the S2-specific T cells from HAtrunc and non-Tg mice appeared to be equally sensitive to stimulation with S2 peptide, and in each case utilized highly diverse T cell receptors to recognize S2-I-Ad. The findings demonstrate that an individual class II-restricted T cell determinant can be recognized as a cryptic self peptide during T cell repertoire formation and as an immunodominant peptide in the context of an anti-viral T cell response, providing a basis for the induction of autoreactive T cells by viruses containing homologs of self antigens.