Background: Cryptosporidium parvum is an obligate intracellular parasite of the Coccidia class that infects the microvilli epithelial cells of the digestive and respiratory systems Objectives: this study aims to detection of the prevalence of cryptosporidiosis among immune compromised children who receive chemotherapy and to compare the three different methods for diagnosis of Cryptosporidium Methodology: 200 children in Aswan oncology institute were enrolled in this study, clinical assessment as well as stool examination by modified Ziehl-Neelsen stain, ELISA assay and Immunofluorescence tests were done. Results: The study showed that the over-all infection was 43.5% by immunofluorescence method, 40.5% by ELISA and 28% by modified Ziehl-Neelsen stain. Infection rate increases in haematological malignancies (AML54.8%, HD46.2 %, ALL41.6%, NON HD 27.3%) than non haematological malignancy (wilms 50%, sarcoma 45.5%, and neuroblastoma 42.9%). Conclusion: Cryptosporidium infection is an important public health problem in Immunocompromised children, raising awareness about cryptosporidiosis has very important effect to decrease prevalence of this parasitic infection.