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. and modified trichrome blue. The obtained result showed incidences of cryptosporidium in naturally infected Friesian calves, 117 (31.67%), 127 (34.33%) and 116 (31.33%) out of 371 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 from 47 postive calves. Safranin-methylene blue staining, Cryptosporidium spp. was found in 20 fecal samples from 47 Friesian calves aged (1-3 months). By using PCR, cryptosporidium specific bands were found in 22out of 47 calves 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.