A novel model for understanding the development and chronicity of autoimmune disease will be proposed. In this approach, treatment is aimed at rebalancing the immune system and removing the driving influence of cross-reactive antigens. Herbs and other measures that can assist in the achievement of these objectives will be outlined. A number of autoimmune diseases including inflammatory bowel disease, myasthenia gravis, rheumatoid arthritis and multiple sclerosis will be discussed in terms of the model and specific phytotherapeutic strategies, backed up by actual case histories.