The flagellum is the organelle providing motility to bacterial cells and its activity is coupled to the cellular chemotaxis machinery. The flagellar filament is the largest portion of the flagellum, which consists of repeating subunits of the protein flagellin. Receptors of the innate immune system including Toll like receptor 5, ICE protease activating factor, and neuronal apoptosis inhibitory protein 5 signal in response to bacterial flagellins. In addition to inducing innate immune responses, bacterial flagellins mediate the development of adaptive immune responses to both flagellins and coadministered antigens. Therefore, these proteins have intensively been investigated for the vaccine development and the immunotherapy. This review describes the utilization of bacterial flagellins for the construction of vaccines against infectious diseases and cancer immunotherapy. Furthermore, the key factors affecting the performance of these systems are highlighted.