Various Cryptosporidium species have been associated with human and animal infections, especially C. parvum infects primarily immunocompromized individuals and causes chronic or acute diarrhea. Outbreaks of human cryptosporidiosis are often cause by the contamination of water supplies with this parasite throughout the world. Because the epidemiological importance it is desirable to develop a sensitive detection technique for this parasite and accurate genetic classification. In this study, we collected samples of whole feces from 256 children with diarrhea at Social Security Children’s Hospital, Ankara, Turkiye. For detecting the oocysts in feces, we used modified acid-fast staining method and direct immunofluorescent assay. For molecular studies, a fragment of the Cryptosporidium COWP and SSU rRNA genes encompassing the hypervariable region was amplified by PCR and then RFLP analysis was performed for distinguishing the Cryptosporidium species in the samples. In RFLP analysis Rsa I, Ssp I and Vsp I enzymes were used to identify the species/genotypes of Cryptosporidium. In the samples studied, we have determined only Cryptosporidium parvum and its two genotypes. The prevalance of Cryptosporidium positivity was about 4.7%.