A 1:1 matched case-control study of calves under 1 month of age was carried out by weekly visits to 7 dairy farms in Mashhad from May 2008 to October 2008. Fecal samples were collected 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 Rotavirus and Coronavirus by a commercial antigen capture ELISA test. Rotavirus antigen was detected in 29.5% and 17% of diarrheic and non-diarrheic calves, respectively and Coronavirus antigen was detected in 2.7% and 1.8% of diarrheic and non-diarrheic calves, respectively. Among diarrheic calves Rotavirus was the most common in the third week of life and Coronavirus was detected only in some cases of second week of life. The excretion of Rotavirus in the feces of scouring calves was significantly higher than in non-diarrheic calves (P value =0.03, odds ratio = 1.9 (1.05 – 3.76)), but there was not any significant association between shedding of Coronavirus in the feces and diarrhea (P value =0.66, odds ratio = 1.4 (0.24 –9.05)). These results indicate that in these industrial dairy farms in Mashhad, infections by Rotavirus can be considered as an important cause for newborn calf diarrhea.