Microbiome is a new research field, and it associated with a variety of chronic autoimmune diseases.The microbiome has received increasing attention as a potential contributing factor to the development of a wide array of immune-mediated diseases, including inflammatory bowel disease, type 1 diabetes mellitus and juvenile idiopathic arthritis.Gut microbiota plays a crucial role in modulating innate and acquired immune responses.The microbiome may influence the development of the immune system, the integrity of the intestinal mucosal barrier, and the differentiation of T cell subsets, and finally resulting in autoimmune diseases.The potential to manipulate the microbiome, might then offer perspectives for future therapeutic interventions.Before such interventions can be thought, a deeper understanding of the cause and effect relationship between these immune diseases and the microbiome is needed to first obtain.Now, the advances in the study of microbiome in immune diseases are discussed.