Some studies can explain how parasitic agents may contribute to the development of autoimmune diseases while others focus on developing a parasite component that may treat autoimmune illnesses. Consequently, the goal of the study was to identify the prevalence of parasitic infections among individuals with various autoimmune disorders and how such infections affect the pathophysiology of these diseases. In the current study, A total of 154 adult patients who had a confirmed diagnosis of autoimmune disease recruited from Menoufia University Hospitals, Egypt, were included. A cross-sectional study design was conducted on the participants who were chosen for history taking, clinical examination, laboratory investigations, and ultrasonography. The results revealed that intestinal parasites such as Enterobius vermicularis, Entamoeba histolytica, Giardia lamblia, and Ascaris lumbricoides were found to be prevalent in 56.5% of the subjects in this study. Immune thrombocytopenia (ITP) patients had intestinal parasites in 100% of cases while parasites were present in 52.6% of autoimmune hemolytic anemia (AIHA) and 47.6% in rheumatoid arthritis (RA) patients. Seroprevalence of toxoplasmosis in the studied cases revealed 15.6% positive IgM and 35.1% positive IgG. The IgM-positive cases were perceived in patients with systemic lupus erythematosus (SLE), Hashimoto thyroiditis (HT), and ITP. Whereas, occurrences of IgG positivity were mainly presented in SLE then AIHA, ITP, and RA patients. Less clinical manifestations were observed in autoimmune disorder patients having intestinal parasitic infections. In conclusion, high parasitic prevalence is common in autoimmune disease patients, which alters the pathogenesis and clinical course of these illnesses.