Lesions suggestive of protozoal infection such as nonsuppurative myositis, nonsuppurative myocarditis, nonsuppurative pneumonia associated with focal cellular necrosis and multifocal necrotizing nonsuppurative encephalitis were observed in 89 (34%) out of 258 aborted bovine fetuses. Immunohistochemistry (IHC) revealed tachyzoites and cysts of Neospora caninum in 55 (61.8%) of these 89 fetuses. Several fetal variables were tested by multivariate logistic regression, in which increasing odds for positivity in IHC were associated with the presence of lesion in the lung (OR=12.11) and less autolytic brain tissue (brain consistency, OR=5.73). However, autolysis in the brain precluded presumptive diagnosis made by histopathology in 53% of the fetuses examined. These results indicate that, when fetal brain is autolyzed, the lung may be adequately used for the presumptive diagnosis of N. caninum infection. The results also confirmed that, even autolyzed, the brain is the most suitable organ for anti-N. caninum IHC.