OBJECTIVE To establish a reliable, rapid, economical method for detection of pestivirus infection in bovine and ovine fetuses and to examine participation of these viruses in abortions and neonatal mortality. METHODS 213 bovine and 31 ovine fetuses, as well as 36 newborn calves and 25 lambs, which had died within 3 days after birth, were tested for bovine viral diarrhea virus (BVDV) and border disease virus by use of different methods. METHODS Detection of BVDV in fetuses was performed by immunohistochemical methods, using a panel of monoclonal antibodies against pestivirus antigens on cryostat and paraffin sections and by virus isolation in cell culture; in some instances, an antigencapture ELISA was performed. Results of the various methods were compared. RESULTS Sensitivity of BVDV detection by immunohistochemical methods and virus isolation in cell culture was equal; however, it decreased in association with autolysis. In autolytic fetuses, use of formalin-fixed, paraffin-embedded brain sections was the most favorable method. Antigen detection by ELISA was less sensitive. CONCLUSIONS Immunohistochemical analysis of cryostat sections of brain, skin, thyroid gland, abomasum, and placenta is a rapid, sensitive method for detecting pestiviruses in fetuses. In the presence of advanced autolysis, this method used on formalin-fixed, paraffin-embedded brain sections is recommended over the other described methods.