Influenza virus infection is associated with type 1 diabetes (T1DM), but its pathogenesis remains unclear. Here, our study found that one of the monoclonal antibodies against H1N1 influenza virus hemagglutinin(HA) cross-reacted with human pancreatic tissue and further demonstrated that it binded to rat islet β-cells. We immunoprecipitated islet protein with this cross-reactive antibody and identified the bound antigen as prohibitin by mass spectrometry. We then expressed the prohibitin protein in bacteria and confirmed the antibody binding to prohibitin by Western blot. We also verified the cross-reactivity of the antibody by prohibitin-siRNA transfection in islet beta cells. We conclude that prohibitin is an autoantigen that cross-reacts with influenza virus HA. The correlation between the autoantigen prohibitin and type 1 diabetes remains to be investigated.