This review provides a comprehensive overview of the relationship between gut microbiota and autoimmune diseases, focusing on systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Sjögren's syndrome (SS), type 1 diabetes mellitus (T1DM), ulcerative colitis (UC), and psoriasis. The gut microbiota plays a pivotal role in maintaining immune balance and homeostasis, and its dysregulation is strongly associated with autoimmune disorders. The review highlights the complex interplay between the gut microbiota, the host, and the immune system, emphasizing the regulatory mechanisms by which the gut microbiota influences autoimmunity and inflammation. Key findings include the impact of gut microbiota on innate and adaptive immunity, the role of short-chain fatty acids (SCFAs) in modulating immune responses, and the potential of probiotics as innovative adjunctive therapies for autoimmune diseases. The review also discusses the clinical significance and potential applications of interventions based on gut microbiota in managing autoimmune diseases.This review provides a comprehensive overview of the relationship between gut microbiota and autoimmune diseases, focusing on systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Sjögren's syndrome (SS), type 1 diabetes mellitus (T1DM), ulcerative colitis (UC), and psoriasis. The gut microbiota plays a pivotal role in maintaining immune balance and homeostasis, and its dysregulation is strongly associated with autoimmune disorders. The review highlights the complex interplay between the gut microbiota, the host, and the immune system, emphasizing the regulatory mechanisms by which the gut microbiota influences autoimmunity and inflammation. Key findings include the impact of gut microbiota on innate and adaptive immunity, the role of short-chain fatty acids (SCFAs) in modulating immune responses, and the potential of probiotics as innovative adjunctive therapies for autoimmune diseases. The review also discusses the clinical significance and potential applications of interventions based on gut microbiota in managing autoimmune diseases.