All pestiviruses are important veterinary pathogens causing economic losses in cattle, sheep and pigs. Besides the important economical losses, pestiviruses may compromise the normal immune response to other pathogens and increase the severity of other infections in sheep. In this study, aborted foetuses (cattle and sheep) in either coastal or inland Black Sea region of Turkey were surveyed for the presence of RNA from pestiviruses (bovine viral diarrhoea virus (BVDV), border disease virus (BDV)). The presence of BVDV RNA was found in 6 of 21 aborted calves (28.57%), although BDV RNA was detected in 14 of 21 aborted lambs (66.66%) by reverse transcriptase polymerase chain reaction. This study also investigates the distribution of viral RNA within the brain, liver and lung of aborted foetuses. The viral RNA positivity rates for the organs varied and were as follows: brain 40.47% and liver and lung 38.09%. The results revealed that pestiviruses are important abort pathogen in the provinces of northern Turkey.