Background: Cryptosporidium, an apicomplexan coccidian protozoan parasite, is a significant cause of diarrhea worldwide especially in children and immuno-compromised that may have subversive consequences and end fatally.Objectives: A cross sectional study, was designed to determine the prevalence of Cryptosporidium in stool of Egyptian children using 4 diagnostic methods; AF stain coproscopy, faecal ICT, Faecal ELISA and nPCR assays and to test their detection threshold compared with PCR as reference standard.A case control study design was implemented to detect the associated risk factors for susceptibility tocryptosporidiosis.Methodology: Stool samples were collected from 250 children divided into 2 groups; 150 diarrheic patients (attending outpatient clinic in Abu El Rish hospital, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt) and 100 apparently healthy. Their relative data were recorded. Samples were processed for copro-parasitological examination with coproscopy of AF stained faecal smear; faecal immunoassays and Copro-nPCR assays.Results: Out of 250 samples 41 were positive for Cryptosporidium with nPCR (18 with ELISA, 16 with ICT and only 14 with AF stain). Using nPCR as a nominated gold slandered, ELISA, ICT and AF stain had 100% specificity and PPV but were of moderate sensitivity, ELISA showed the highest sensitivity (43.9%), followed by ICT (39%) while AF stain reported the lowest sensitivity (34%). Multi-attribute analysis ranked nPCR the highest one for laboratory use followed by AF stain, ICT and lastly ELISA. Estimating the study variables as risk factors only the type of stool was a risk factor.Conclusion: Cryptosporidium is an important enteric pathogen among both diarrhoeic and non-diarrhoeic Egyptian children with a clearly high prevalence of 16.4%. Conventional methods for detection of Cryptosporidium infection; coproscopy and faecal immunoassays are very 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 majority of Cryptosporidiuminfections were significantly detected in soft stool, which gave 2 times yield more than liquid stool. The proper choice among faecal testing alternatives needs collaboration between clinicians and lab for a superior patient care.