This chapter discusses various therapeutic challenges of autoimmune diseases. In many cases, the disease is severe enough to significantly reduce longevity. In other cases, the disease causes major handicaps and discomfort that justify the usage of aggressive treatments generating their own hazards. Present treatments are palliative, anti-inflammatory, or immunosuppressive without any specificity for the pathogenic mechanisms of the disease. With a few exceptions, the treatment of autoimmune diseases has not significantly evolved from the mid-1980s. Therefore, much attention is drawn to modern technologies that have made new agents available. These approaches have been the matter of extensive experimental studies in the numerous and diversified animal models of autoimmune diseases. Some of them have already been tested in the clinic and even approved by regulatory authorities. The chapter reviews these strategies with particular emphasis on agents or methods that have entered the clinical arena. In addition, it is interesting to discuss how lessons drawn from the development of novel therapeutic strategies in one particular autoimmune disease may be translated into beneficial therapies for other autoimmune conditions.