Stool samples from 182 diarrhoeic (symptomatic) children and 100 apparently healthy (asymptomatic) children, matched for age, from Aboul-Reesh Cairo University Pediatrics Hospital were examined by ELISA and by nPCR (targeting COWP gene) for the detection of Cryptosporidium. The demographic and environmental data of the diarrhoeic group was recorded. The PCR amplified product of positive cases was then subjected to RFLP by digesting it with the restriction enzyme RsaI. The obtained fragments were resolved by electrophoresis and the bands were visualized and characterized versus a standard. ELISA results demonstrated a prevalence rate of 13.2% (24/182) among diarrhoeic group, and 8% (8/100) among nondiarrheic group, with overall detection rate of 11.3% (32/282). Higher rates of detection were obtained by nested PCR assay among diarrhoeic group 25.8% (47/182) and 16% (16/100) among non-diarrhoeic group with overall detection rate of 22.3% (63/282). Considering nPCR as the reference method, ELISA had a sensitivity of 47.6% and a specificity of 99.1%. RsaI digestion of nPCR product of COWP gene revealed the presence of 2 genotypes: genotype 1with 4 bands (34, 106, 125 and 285) and genotype 2 in which 3 bands (34, 106 and 401). Among the 63 cases with cryptosporidiosis, 53 (88.3%) had genotype 1, and 7 (11.7%) had genotype 2. The higher prevalence of genotype 1 suggests a relatively greater risk of human source of infection than zoonosis.