Brucellosis and Q fever, two zoonoses, are important causes of abortion in ruminants, as well as economically significant diseases caused by a gram-negative bacterium. Determination of these diseases is therefore of great importance. In this study, the organs of 35 naturally infected and aborted ovine fetuses were examined for the presence of changes resulting from infections by Brucella melitensis and Coxiella burnetii, according to macroscopic, bacteriological, histopathological and immunohistochemical methods. B. melitensis was observed in 21 cases, and C. burnetii was observed in 8 cases of the aborted ovine fetuses, and these were determined with immunohistochemical methods. Brucellosis was observed in 18 of the aborted ovine fetuses, and this was determined by microbiological methods. Negative (-) results were found for all of the other fetuses. The Brucella antigen was determined to be localized as intracytoplasmic in mainly alveolar macrophages, bronchi, bronchioles, glandular epithelial cells around bronchial glands, neutrophils, hepatocytes and Kupffer cells. The Coxiella antigen was found to be localized in the alveolar macrophages in the lungs, bronchi, bronchioles and alveolus, and in the cytoplasms of bronchial gland epithelial cells, and in the cytoplasms of hepatocytes and Kupffer cells in the liver. Immunohistochemical and microbiological diagnoses of brucellosis and coxiellosis were compared; it was concluded that immunohistochemical methods were more safely applied than microbiological methods.