Basophils are the rarest blood cell population and have not been extensively studied. Our understanding of the functions of basophils is limited to their roles as the main effector cells in hypersensitivity reactions. Similar to mast cells, basophils express high-affinity IgE receptor (FcεRI), contain granules, and release hypersensitivity-associated mediators (such as histamine). The roles of basophils have not been fully elucidated; however, with the rapid development of monoclonal techniques, high-purity cell sorting techniques, and basophil-deficient mouse models, understanding of the functions and phenotypes of basophils has increased. This facilitates further investigations on the relationships between basophils and host immunity. Basophils are not only involved in mediating the generation of allergic reactions but also play important roles in immunomodulation and are responsible for the onset of infectious, allergic, and autoimmune diseases. In this review, we summarize the progress in understanding the roles of basophils in mediating immune responses with an emphasis on autoimmune diseases, particularly systemic lupus erythematosus and rheumatoid arthritis.