Previously regarded solely as a digestive entity, the human gut has been revealed to harbor a rich diversity of microbial flora, pivotal in maintaining overall health and organ functionality. Contrary to conventional wisdom, certain microbes confer notable benefits rather than posing threats. The gut microbiota, consisting of Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, plays a crucial role in health maintenance, and dysbiosis can precipitate disease onset. Autoimmune disorders stem from immune system dysregulation, resulting in self-cell attacks. Recent microbiome research underscores a correlation between altered gut microbiota and autoimmune diseases. This chapter delves into the impact of the gut microbiome in autoimmune diseases and presents gut microbiome targeting therapy as a possible treatment alternative.