BACKGROUND: Today, Cryptosporidium is considered as one of the etiological agents of diarrhea syndrome in newborn ruminants, especially calves. OBJECTIVES: The incidence rate of the infection to this parasite in diarrheic calves in southern Khorasan, Neishabour was studied. METHODS: One hundred seventy fecal samples of diarrheic calves from husbandries in Neishabour were collected from July 2009 to January 2010. These samples were transferred to laboratory and were examined for the presence of Cryptosporidium oocyst after concentration with formol-ether method and modified Ziehl-Neelsen staining. RESULTS: The incidence rate of infection to this protozoan in the studied samples was 11.2%. Moreover, 13.04% of male calves and 8.97% of female animals were infected with the parasite. The incidence rate of the infection in cold season (14.06%) was more than warm season (9.43%). Meanwhile, 12.12% of the calves under three months of age and 7.89% aged three to six months were infected with protozoan. Statistical analyses did not show significant relationship between the infection of parasite and the studied factors including age, sex, and season. CONCLUSIONS: Control of Cryptosporidium is necessary, with regard to the presence of this parasite in calves of Neishabour and its zoonotic aspect.