Epigenetic deregulation has become a major topic in biomedical research. Most of the information currently available in the field comes from the study of epigenetic alterations in cancer, particularly in haematological malignancies. The recognition of the epigenetic component of autoimmune diseases in conjunction with the existence of common genes underpinning pathways that are crucial to the development of autoimmunity and haematological cancers, facilitates interaction between these two areas of research. Here, we examine what is presently known from epigenetic studies of autoimmune diseases, how epigenetic alterations in haematological malignancies can be used to better understand mechanisms of epigenetic deregulation and how they might be used in epigenetic therapy to treat autoimmune diseases.