Swine influenza virus (SIV) is a prevalent respiratory pathogen in pigs that has deleterious consequences to animal health, production, and public health. Pigs represent an important reservoir for influenza as well as a potential mixing vessel for novel gene reassortments. Despite the central role of the pig in the 2009 pandemic and 2012 variant H3N2 outbreak, much remains unknown about the impact of swine immunity on SIV transmission, pathogenesis, and evolution. An incomplete understanding of interactions between the porcine immune system and SIV has hindered the development of new diagnostic tools and CD8+ T cell influenza epitope based vaccines. In order to address this gap in knowledge, we identified swine leukocyte antigen (SLA) restricted influenza virus peptides presented by swine respiratory epithelial cells using an immunoproteomics approach. The majority of MHC associated peptides belonged to matrix 1, nucleocapsid, and nonstructural 1 proteins. Specific epitopes, such as M1229-242, NS177-89, and NP417-426, may have value in epitope based vaccines. Future investigations examining the potential cross-reactive nature of these peptides are needed to confirm antigen recognition by cytotoxic T lymphocytes and utility as vaccine candidates.