The present study aimed to investigate the presence and prevalence of Cryptosporidium among immunocompromised patients in Wasit Hospitals and health centers to determine the best method for its diagnosis. The study started from the 1st of August to the end of November 2020. One hundred forty stool samples were collected from immunocompromised patients from both genders who attended the hospital and health centers at Wasit province. Stool samples were inspected by modified acid-fast stain as a standard method, enzyme linked immunosorbent assay (ELISA) and Molecular Nested PCR method. Modified Ziehl-Neelsen technique revealed 46 (33%) positive cases for Cryptosporidium oocysts, of 85 males and 55 females, highly significant relationship was found between the genders and between different age groups of infection with a highly significant difference between rural and urban area. The prevalence of Cryptosporidium was 57.14% using nested PCR and 38.46% for ELISA in comparison with MZN method. It is concluded that cryptosporidiosis found to be endemic in Wasit Province for the first time and the nested PCR was the most reliable technique for its diagnosis.