In this study, clinical, parasitological, macroscopical, histopathological and immunohistochemical examinations were performed on 19 kids and 11 lambs (30 animals) with neonatal diarrhoea to detect the presence of Coronavirus, Cryptosporidium parvum and Giardia intestinalis. Clinically, severe dehydration, yellowish-green to brown coloured diarrhoea and death were observed. Mortality rates were 10-30% in the examined flocks. The most common agent was C. parvum diagnosed in 20 animals as a single causative agent, whereas G. intestinalis was found in 5 of 30 animals. These two protozoa were detected together in 4 animals upon faeces examination. Fifteen of 24 cases of C. parvum and 3 of 11 cases of G. intestinalis were also confirmed histopathologically. Following immunohistochemical examination, all cryptosporidiosis cases were confirmed by positive immunostaining of intestinal sections. Two additional Giardiosis cases with negative results upon parasitological and histopathological examinations were diagnosed by means of immunohistochemical examination. Coronavirus was detected immunohistochemically in one kid with neonatal enteritis. Following diagnosis, herds were treated with Trimethoprim + Sulfodoxine and multivitamin complexes. Intravenous and intramuscular administrations of these drugs were effective for both treatment and prevention of neonatal diarrhoea in lambs and kids.