Cryptosporidiosis infection could be considered as a causative agent of diarrhea in 60.69 of pre-weaned calves. Diarrhea in beef cattle has an important impact in economic productivity. Infectious diarrhea is mainly caused by four agents: Enterotoxigenic Escherichia Coli (ETEC), Rotavirus, Corona virus and Cryptosporidium parvum. The aim of the study was to compare Microscopy staining method and polymerase chain reaction (PCR) as methods for diagnosis of Cryptosporidium species. Fecal samples were collected from three hundred and seventy one naturally infected Friesian calves. Fecal smears stained by the modified Ziehl-Neelsen technique showed that the oocytes appeared as acid fast (red-pink) on a green background and by using of Safranin-methylene blue staining technique, the oocysts appeared orange in color on a blue background, while the oocysts appeared pink with dark granules when stained by modified trichrome blue. The incidence of cryptosporidium in naturally infected Friesian calves was 117 (31.67%), 127 (34.33%) and 116 (31.33%) out of 371 friesian calves examined by Modified Ziehl-Neelsen technique, Safranin-methylene blue and modified trichrome stains respectively. Safraninh-methylene blue staining is better technique if compared with Modified Ziel-Neelsen technique and modified trichrome technique. By using Safranin-methylene blue staining, Cryptosporidium spp.was found in 10 fecal samples from 47 Friesian calves (1-3 months age). By using PCR, cryptosporidium specific bands were found in 22 of these cases. It can be concluded that microscopic staining method, which can be used as a diagnostic method has some limitations, while, PCR is more sensitive and specific, which allows the identification of parasite oocyst.