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Autoimmune diseases are characterised by the immune system’s attack on the body’s own tissues. These conditions affect an increasing number of people worldwide, predominantly women. Loss of tolerance to self-antigens can occur in virtually all of the body’s organs and systems, including digestive (e.g., type 1 diabetes, inflammatory bowel disease), endocrine (e.g., Grave’s disease, Addison’s disease), and neurological (e.g., multiple sclerosis, autoimmune epilepsy), as well as connective tissue (e.g., rheumatoid arthritis, spondyloarthritis). While autoimmunity has been linked to genetic and epigenetic factors as well as to a range of environmental triggers such as pathogens and drugs, the underlying causes of many of these conditions remains incompletely understood. This Collection will highlight articles on all aspects of autoimmune diseases, including their etiology, epidemiology, diagnosis, and treatment.