The hygiene hypothesis has been implicated in the dramatic increase in autoimmune and allergic diseases noticed in recent decades, especially in developed countries. This growth was associated with lesser exposure to diverse immunoregulatory infectious agents. This hypothesis has been proved by many potent epidemiological and experimental studies. The results of these studies along with the analysis of the western world's microbiome helped us to have a greater idea about microorganisms shared in the hygiene hypothesis, as well as their main mechanisms that have an effect on the immune system. Protozoal infections have been proved to have remarkable immunomodulatory changes in different autoimmune diseases. Helminths and their derivatives were proved to have a protective role. Helminths' broad immunomodulatory effects have been tested in clinical trials of autoimmune diseases, including inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, and type-1 diabetes. In this review, we discussed particular parasitic infections and their immunomodulatory effects on some autoimmune diseases.