Introduction Autoimmune disorders are characterized by increased immune reactivity and by the presence of antibodies against the own structures of the body. Microbiota is defined as the presence of commensal microorganisms in the body and its interaction with the physiological processes that drive human life. Methods A literature search was performed by independent investigators using Web of Science, PubMed-MEDLINE, Google Scholar, and other search services with the following keywords and word combinations: "microbiota", "systemic autoimmunity", "lupus erythematosus", "diet", "autoimmune arthritis", and "autoimmune encephalopathy". Inclusion criteria included relevant articles in English and French, published between 1st January 2011 and 1st May 2018 that addressed autoimmune diseases and microbiota involvement as their main theme. Exclusion criteria were case reports, unavailability of any full article, unclear presentation, non-relevant studies and reports of different languages other than English or French. Results Recent studies have shown an important link between autoimmune disorders, such as lupus erythematosus, antiphospholipid syndrome, rheumatoid arthritis or type 1 diabetes mellitus, and gut microbiota. This link, correlated with the major changes in diet and with the antibiotic abuse of the last decades, may explain the peak in the incidence of autoimmune disorders in the last years. Moreover, commensal microbiota directly interacts with the immune system by influencing the immune-commensal axis, which differentiates commensal microorganisms of the body from pathogens from outside of the organism. Conclusions When imbalance of the axis develops, the autoimmune process against organs with a commensal population is triggered. New therapies directed against the modified microbiota appear to be beneficial in the control of autoimmune disorders.