Objective: To investigate the relationship of Cryptosporidium and immunological parameters among children with malignant diseases. Methods: Stool samples were collected from 101 children with malignant disease and 107 apparently healthy children. Direct smear method and then formalin-ether sedimentation method were done for all stool samples to identify intestinal parasites. Fecal smears were prepared from the sediment and stained by the modified Ziehl-Neelsen method for the recovery of acid-fast oocysts of Cryptosporidium. Phagocytic activity, complement C3 and C4 estimation, immunoglobulin levels and CD3, CD4, CD8, CD19 marking and phenotyping were carried out for 30 patients with acute lymphocytic leukemia (ALL) and 20 control group. Results: ALL was the major type (47.52%) of malignant cases in the studied subjects. The other type ranged from 0.99% to 10.9%. Out of the 101 patients, 50(49.5%) were found to be positive for intestinal parasites compared to 13(12.15%) of the control group (P<0.01). Cryptosporidium oocysts were found to be excreted by 10(9.0%) patients and 1(0.93%) of the control group (P<0.01). The phagocytic activity, levels of IgM, IgA, IgG and CD3, CD4 cell numbers were lower in patients than in control group while higher in case of C3, C4, CD8 and CD19. Conclusion: Children with malignancy are immunocompromised. Therefore, Cryptosporidium and other intestinal parasites must be considered in the differential diagnosis in this risky group in order to reduce the suffering often faced by those children.