Cryptosporidiosis is a parasitic disease caused by the cryptosporidium protozoan in vertebrate animals. In livestock, especially ruminants, infants develop diarrhea syndromes. The infection is widespread throughout the world, as well as in Iran, which is reported from various species. Morphological diagnosis of Cryptosporidium species has many limitations and is of no taxonomic value alone, therefore using molecular methods helps remove these limitations to some extent. The current study is aimed at microscopic, molecular, and antigen detection and isolation of Cryptosporidium Parvum parasite. Firstly, there were 300 specimens collected from different parts of Iran. Next, purification of oocysts from feces was carried out according to the method of Casemore et al., through the flotation technique following which staining was done by means of the modified Ziehl-Neelsen method (Henriksen method), and identification through diagnostic keys. ELISA test was also performed on the specimens for which the results were from 1 positive to 4 positive. Results of our study demonstrated that from the 300 cases tested for Cryptosporidium through the molecular method, 48 cases (16%) were positive. These cases were collected during summer, autumn, and winter, however, more than 50% of positive cases were found among specimens collected in autumn. Furthermore, there were 54 positive cases found by means of PCR test, which indicates 6 cases more than that for ELISA results. Finally, results from PCR detection and ELISA, were subjected to Chi-Square analysis, where no significant difference between the collected data was observed (p=.0587).