Cryptosporidium is a genus of zoonotic pathogens transmissible from a variety of animals to humans and is a considerable public health concern. It is a significant cause of diarrheal disease in developing and industrialized nations. Cryptosporidium parvum and Cryptosporidium hominis are the main agents of cryptosporidiosis in humans. In this study we identified the genotypes of the Cryptosporidium isolates from clinical samples from diarrheic children using polymerase chain reaction (PCR) amplification and restriction fragment length polymorphism (RFLP) analyses of the TRAP-C2 gene (Thrompodin Related Adhesive Protein). A total of 430 fecal specimens from 1 to 14 years children were collected from inpatient and outpatient clinics of Benha University, Educational and Children Specialized Hospitals, Benha, Qalubyia, and were microscopically examined for Cryptosporidium spp. All infected samples were also analyzed using nested PCR. A polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the (266-366 bp) of TRAP-C2 gene was also used to detect and identify Cryptosporidium spp. in PCR- positive samples. The results showed that 50 (11.63%) of the specimens were positive for Cryptosporidium spp. Genomic amplification and restriction digestion of the PCR products by BstETI, Hae III for TRAP-C2 gene restriction enzymes revealed that 82% (41/50) had C. parvum, 12% (6/50) had C. hominis, and three (3/50) samples (6%) had mixed infections. In conclusion, elevated prevalence of C. parvum, suggesting animal-human (zoonotic) transmission and further investigations are required to determine the subgenotypes of C. parvum to clarify the mode of transmission in order to improve the control measures.