Background:Cryptosporidium is a protozoan parasite that causes gastrointestinal infection. Each cryptosporidial species usually inhabits a particular host; however cross-infectivity could occur. Objectives: The aim of the study was to identify prevalent Cryptosporidium species among a sample of immunocompetent and immunocompromised children. Subjects and Methods: This study included 150 children divided as 50 control group (apparently healthy with no complaints) and 100 patients (immunocompetent and immunocompromised) with gastrointestinal manifestations. Stool samples were collected and examined microscopically using modified Zeihl-Neelsen stain (mZN), ELISA for coproantigen and nested PCR (nPCR). Restriction fragment length polymorphism (RFLP) technique was done for species identification of PCR products. Results: Among the 100 patients, cryptosporidiosis prevalence was 34%, 46% and 59% as detected by mZN, ELISA and nPCR, respectively. Infection was more prevalent in immunocompromised group (84%) than immunocompetent group (34%) as detected by nPCR (P<0.001). Cryptosporidiosis was found to be significantly associated with nausea (P=0.002) and with diarrhea (P=0.04). Detected species among studied children were C. hominis (52.5%), C. parvum (33.9%), C. meleagridis (8.5%) and C. felis (5.1%). C. hominis was the prevalent species in both immunocompetent and immunocompromised groups. Conclusion:C. hominis was proven to be the more prevalent species among cryptosporidiosis positive children in this study. More attention should be paid to this emerging parasitic infection especially in immunocompromised children.