A cross-reactive cytotoxic T lymphocyte clone was produced by stimulation with a hybrid protein that contained a portion of the NS1 and the HA2 subunit of A/PR/8/34 (H1N1) virus. Transfer of this clone clears virus from the lungs of mice challenged with H1 or H2 viruses. In these experiments we define the location of the protective CTL epitope to the transmembrane portion of the influenza A virus hemagglutinin which is well-conserved on H1 and H2 subtype viruses. The H1 and H2 cross-reactive CTL clone recognized a synthetic peptide of 23 amino acids (anchor peptide) corresponding to the transmembrane domain of the A/PR/8 (H1) HA as well as the comparable anchor peptide of the A/JAP (H2) HA. The anchor peptide of the A/PR/8 HA competed against the anchor peptide of A/JAP HA in cold target inhibition tests. These results indicate that the epitope recognized by the cross-reactive CTL is located on the transmembrane region of both A/PR/8 HA and A/JAP HA. We prepared synthetic peptides to define the epitope within the transmembrane region of A/PR/8 HA which is recognized by a cross reactive CTL clone. The results indicate that residues 518-528 in the transmembrane region of A/PR/8 HA contain the cross-reactive CTL epitope.