There is generally no cure for autoimmune disorders, but the symptoms can be managed. Currently available drugs/treatments are more potent than those in the past decades. However, finding the right drug and right patients has remained a serious problem. We should revise our diagnosis criteria to more accurate ones. During the recent years, personalized medicine has attracted much attention. However, it needs to be well-explained for autoimmune diseases. Personalized medicine aims to find the most optimum drugs for a patient. Hence, recognizing the drugs based on genetics and molecular profile of patients, needs a comprehensive protocol. This study attempted to discuss the most practical and effective ways for identifying right patient and right drug. Patients should be divided into subpopulations. According to the last diagnosis criteria and therapeutic options, it was attempted to highlight the gaps or contradictions in current understanding and suggest what the future of research in this area may hold. Various factors could be considered, including genes variants, genes expression, epigenetic alterations, immune responses, and also basic and obvious characteristics (sex, age, ethnic, etc.). Moreover, advantages, disadvantages, obstacles, and opportunities during the personalized medicine for auto immune diseases have been discussed in great detail. Finally, creation of a global library that covers all the aspects of personalized medicines for different types of autoimmune disease was suggested. In conclusion, revising diagnosis and treatments of autoimmune diseases toward personalized medicine could be the revolutionary step for having more effective and safer therapeutic options.