Autoimmune diseases are characterized by aberrant immune responses against healthy cells and tissues. However, the exact mechanisms underlying the development of these conditions remain unknown. CD4+CD25+ regulatory T cells (Tregs) are a subset of mature T cells which have an important role in maintaining immune homeostasis and preventing autoimmune diseases. Forkhead box p3 (Foxp3), a member of the fork head transcription factor family, is recognized as a marker of CD4+CD25+ Tregs. The decreased number and/or function of CD4+CD25+ Tregs in peripheral blood and related tissues has been demonstrated in systemic lupus erythematosus, systemic sclerosis, and other autoimmune diseases, which are at least partially regulated by epigenetic mechanisms. Epigenetics refers to the study of potentially heritable alterations in gene expression without underlying changes of the nucleotide sequence, mainly including DNA methylation, histone modification, and microRNAs (miRNAs). For example, DNA methylation status of CpG islands on the Foxp3 gene, which may be affected by normal aging and regulated by environmental factors, plays an important role in modulating the homeostasis of Foxp3 expression in Tregs. Foxp3 gene in Tregs also shows distinct acetylation and trimethylation levels of histone H3 and H4 when compared with effector T cells, leading to an open chromatin structure. MicroRNAs such as miR-155, miR-126, and miR-10a also exert an important influence on the differentiation, development, and immunological functions of Tregs. Aberrant epigenetic modifications affecting Foxp3 and other key genes in Tregs contribute to disease activity and tissue inflammation in autoimmune diseases, which holds great potential for providing novel targets for epigenetic therapies. Advances in research into the epigenetic regulation of CD4+CD25+ Tregs may also lead to the identification of new epigenetic biomarkers for diagnosis and prognosis.