Background: Cryptosporidium is a single-celled protozoa that belong to the kingdom Protozoa, Although it can cause mild to severe diarrhoea, However, immunocompromised individuals may be unable to clear the parasites and, therefore, suffer chronic and debilitating illness.Objectives: The primary outcome of the present work was immune-molecular detection of Cryptosporidium among group of Egyptian children by detection of Cryptosporidium copro-antigen using ELISA (Enzyme linked immunosorrbant assay) and copro-DNA using nested polymerase chain reaction (nPCR) with validation of used diagnostic tests and to identify Cryptosporidium genotypes using restriction enzyme to digest nPCR product by PCR-restriction fragment length polymorphism (PCR-RFLP). The second outcome was analysis of collected data variables as an exposure for susceptibility to detect Cryptosporidium and its genotypes among diarrhoeic children.Methodology: Stool samples were collected from 282 children (divided into 2 groups; 182 diarrheic patient and 100 apparently healthy) attending outpatient clinic in Abu El Rish hospital, Kasr Al-Ainy School of medicine, Cairo University, Cairo, Egypt. Their relative data were recorded. Samples were processed for, faecal immunoassays, Copro-nPCR assays and Cryptospoiridum genotyping using PCR-RFLP.Results: of 282 samples 63 was positive for Cryptosporidium with nPCR (32 with ELISA). Using nPCR as a nominated gold slandered, ELISA had 99.2% specificity and 47.6% sensitivity. Using the restriction enzyme Rsa I, 53(84.1%) had genotype 1, and 7 (11.1%) had genotype 2, and three cases could not be digested by Rsa I restriction enzyme. Risk assessments among the diarrheic group could not show any significant association.Conclusion: Cryptosporidium is an important cause of diarrhea among Egyptian children with a prevalence of 22.3%. Although diarrhoea is the most common symptom of Cryptosporidium infection, asymptomatic cryptosporidium infection was detected among non-diarrhoeic children with a prevalence of 16%. faecal immunoassays are specific but their sensitivity showed that they were not sufficient to be used as a consistent single detection method with many infections may escape the detection. Cryptosporidium Copro-DNA detection using nPCR was of higher sensitivity and specificity and going to replace conventional methods for reliable detection of Cryptosporidium. The COWP nPCR and RFLP assay proved to be useful for diagnosis and genotyping of Cryptosporidium. Both genotype 1 and genotype 2 are implicated in Egyptian children.Genotype 1 was found to be relatively more prevalent than genotype 2 among all groups of patients examined, suggesting a relatively greater risk of human source of infection than zoonosis