Cytotoxic T lymphocyte (CTL) responses against influenza A virus in C57BL/6 mice are dominated by a small number of viral peptides among many that are capable of binding to major histocompatibility complex (MHC) class I molecules. The basis of this limited immune recognition is unknown. Here, we present X-ray structures of MHC class I molecules in complex with two immunodominant epitopes (PA_224–233/D^b and PB1_703–711/K^b) and one non-immunogenic epitope (HA_468–477/D^b) of the influenza A virus. The immunodominant peptides are each characterized by a bulge at the C terminus, lifting P6 and P7 residues out of the MHC groove, presenting featured structural elements to T-cell receptors (TCRs). Immune recognition of PA_224–233/D^b will focus largely on the exposed P7 arginine residue. In contrast, the non-immunogenic HA_468–477 peptide lacks prominent features in this C-terminal bulge. In the K^b-bound PB1_703–711 epitope, the bulge results from a non-canonical binding motif, such that the mode of presentation of this peptide strongly resembles that of D^b-bound peptides. Given that PA_224–233/D^b, PB1_703–711/K^b and the previously defined NP_366–374/D^b epitopes dominate the primary response to influenza A virus in C57BL/6 mice, our findings indicate that residues of the C-terminal bulge are important in selection of the immunodominant CTL repertoire.