Influenza infection can cause mild to severe illness and can even lead to death. The best way to prevent infection is vaccination against influenza. Complications of influenza infection are not only a consequence of acute infection but can also present as late autoimmune response. Influenza is not frequently implicated as a trigger for autoimmune diseases, but case reports of autoimmune adverse events have been published even following influenza vaccination. In this article we review published data on autoimmune diseases following influenza infection and vaccination. We also discuss immunity of influenza infection in connection to pathogenesis of autoimmune response and autoimmune disease.