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Immune system overactivity leads to own tissue damages, which result in autoimmune diseases (AIDs). It seems that several variables, including genetics, epigenetics, and environmental factors, trigger autoimmunity. Investigations on autoimmune diseases in identical twins have shown that genetic factors are not the only risk factor for disease susceptibility (due to incomplete concordance). This issue suggests that epigenetic mechanisms, including DNA methylation, histone modifications, and noncoding RNAs (mainly miRNAs), might be involved in the pathogenesis of autoimmune diseases. Indeed, epigenetics describes how environmental factors influence the expression of gene without any changes in DNA sequences. In this chapter, we have reviewed the epigenetic alterations in various autoimmune diseases and environmental factors that stimulate these epigenetic alterations. So, we attempt to clarify how …