This study was aimed at determining the existence of Neospora caninum and Toxoplasma gondii in aborted bovine foetuses. In this research, 102 bovine foetuses were examined by duplex PCR, immunohistochemistry and immunofluorescence to determine the presence of N. caninum and T. gondii. None of the aborted bovine foetuses were shown to have T. gondii, but N. caninum was detected in 26 foetuses (25.49%) by duplex PCR, in 18 (17.64%) by immunohistochemistry and in 8 (7.84%) by immunofluorescence. Moreover, 16 livers, 13 kidneys, 12 spleens, 8 thymuses and 5 brains of the 18 foetuses examined by immunohistochemistry showed immunopositivity. Positive staining was found in the spleen of eight foetuses by the immunofluorescence method. In this study, immunohistochemistry was shown to be superior to immunofluorescence in terms of diagnosis. Although immunofluorescence has the advantage of being the easiest to use in practice, it makes diagnosis more difficult because of its non-specific staining.