Autoimmune diseases are diseases caused by loss of tolerance to self-antigen by own immune system. In normal physiology, both cellular and humoral components of immune system recognized foreign antigens and rapidly destroyed invading antigens. Finally, immune system kept memory of characteristics of foreign antigens. Immune system is tolerant to self-antigens and maintains homeostasis during our defense against micro-organisms. Once the tolerance was broken by environmental, genetic and unknown factors, our immune system started to target self-tissues by using antibodies, cytokines and even killer cells to mount inflammatory responses. Diseases such as rheumatoid arthritis, systemic lupus erythematous, psoriasis, Crohn’s disease, vasculitis and multiple sclerosis were known for the presence of autoimmune responses to self-antigens. Inhibitors of cytokines such as tumor necrosis factor, interleukin 6, interleukin 1, interleukin 17 were developed in the last decade to treat various autoimmune diseases. In addition, target molecules on the cell surface such as CD20, BLys on B lymphocytes, and CTLA-4 on T lymphocytes were also used to treat diseases with immune dys-regulation. Furthermore, small molecules inhibit messengers of intracellular sign transduction such as Jak kinase, Syk kinase are ready for launch to combat more diseases. In conclusion, target therapies are becoming a main stream for the treatment of autoimmune diseases.