In areas where helminth infections are common, there is a low prevalence of autoimmune diseases. This observation gave rise to the hygiene hypothesis, claiming that certain organisms which were abundant in the human microenvironment hold an immunoregulatory and immunosuppressive effect, therefore, their eradication led to an increase in immune mediated diseases. This hypothesis laid the foundation for several directions of research which demonstrated an immunosuppressive and immunoregulatory effect of helminths on both the acquired and the innate immune systems. These studies led to the examination of the therapeutic potential of helminths and their components in treating different autoimmune diseases such as inflammatory bowel disease, rheumatoid arthritis, multiple sclerosis, and systemic lupus erythematosus. The administration of helminth products in murine models of these diseases exhibited a positive effect on disease expression, morbidity and mortality, as well as the ability to prevent the onset of disease to some extent (when given in a preventive protocol). Recently, a synthetic molecule composed of phosphorylcholine (a product of the nematode a. vitae) combined with the protein tuftsin, which is produced by human splenocytes, was shown to exert the aforementioned positive effects on a murine model of systemic lupus erythematosus (SLE). These discoveries point to a new direction in research for developing helminth-based therapies for autoimmune diseases.