A 1:1 matched case-control study of calves less than 1 month of age was carried out by weekly visits to some dairy farms in Mashhad, Iran. Fecal samples were collected over a 6-month period from a total of 112 calves with clinical signs of diarrhea and from 112 matched animals without clinical signs of diarrhea as assessed by a scoring system. The samples were investigated for the presence of Cryptosporidium spp. oocysts by modified Ziehl–Neelson staining method. Cryptosporidium spp. oocysts were present in 51.8% of calves with diarrhea and in 21.4% of the controls. Among diarrheic calves, the highest prevalence of Cryptosporidium oocyst shedding was in age group 8–14 days (74.5%), and the lowest prevalence of Cryptosporidium oocyst shedding was in age group 22–30 days (23.8%). The McNemar test in all sampled calves showed significant differences in odds ratio for the presence of Cryptosporidium spp. in fecal samples, and the excretion of parasite in the feces of scouring calves was significantly higher (odds ratio 6.1) than in healthy calves. Differences between animals with and without diarrhea were statistically significant for age groups 1–7 and also 8–14 day-old calves. These results indicate that in these industrial dairy farms in Mashhad, infections by Cryptosporidium should be considered as a potential cause for newborn calf.

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