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Cryptosporidium is a parasite that has the potential to cause complications in Immunosuppressed patients such as beta-thalassemia. Thus, Stool and blood samples were collected from 260 patients with beta-thalassemia who consulted the Thalassemia Center at Azadi Hospital, and from 110 individuals suffering from watery diarrhea, abdominal pain, or any digestive disorder, returning to the pediatrics Hospital and Kirkuk General Hospital, during October 2019 until September 2020. The rate of parasite infection reached (16.92%) in Thalassemia patients, while it reached (14.45%) in the other examined samples, and the rate of infection of males was (17.9%) higher than females (14.4%). The study showed a significant decrease in hemoglobin (Hb), red blood cell count (RBC) and mean cell volume (MCV), and a significant increase in white blood cells (WBC), which may reflect higher neutrophils and lymphocytes in patients with beta-thalassemia infected with the parasite than in other samples. Lipid profile showed a decrease in the level of total cholesterol (TC), low-density lipoproteins (LDL), and high-density lipoproteins(HDL), and a significant increase in the level of triglycerides(TG), liver function enzymes Alanine aminotransferase (ALT), Aspartate transaminase (AST). Besides, Alkaline phosphatase (ALP) enzymes and the level of ferritin (Fe) in thalassemia patients infected with the parasite compared to the other samples. the C-reactive protein CRP level was significantly higher, as a result of infection with the parasite. It was concluded that patients with beta-thalassemia have multiple abnormal complications as a result of multiple blood transfusions, iron overload, and hepatitis. These complications are risk factors causing parasite infection such as Cryptosporidiosis.