The present study was conducted on 120 newly born calves (37 mixed breed, 66 native breed and 17 buffaloes calves), aged from one day to 6 months, they examined during the period from April 2014 to April 2016, these animals belong to some villages and farms from Assiut governorate. The overall prevalence was15.83 % (20.89% in calves less than two months, 11.36% in calves' from 2-4months with no infection rate from 4-6 months).the prevalence of Cryptosporidiosis in village shad higher rate of infection (19.23%) than farms (9.52%) in Assiut governorate. Mixed breed calves were more susceptible (24.32%) than native breed calves (13.64%) followed by buffalo calves (5.88%). Male calves were more susceptible than female calves to infection {males 16.44% (12/73) – females 14.89% (7/47)}. The clinical findings of cryptosporidiosis in examined calves were showed mild to severe diarrhea with varying degree of dehydration. Some cases were feverish. The state of appetite was different according to the severity of illness. The feces were varied from pasty to watery in consistency, pale yellow, yellow or greenish in color and sometimes contained mucous and blood. Higher infection rate was in non-hot months (22.95%) than hot months (8.47%). The molecular technique used for identification of Cryptosporidium infection in calves was nested PCR which is highly sensitive as a diagnostic tool for cryptosporidiosis and allow a rapid diagnosis in outbreak situations and provide information on genotypes.