Blood samples from 3112 sheep (185 flocks) and 1196 goats (163 flocks) from the Western region of Austria were tested for pestivirus-specific RNA. In this area, communal Alpine pasturing of sheep, cattle and goats is an important part of farming. The prevalence of sheep persistently-infected (PI) with pestivirus was 0.32% (10 animals) and the PI animals originated from five flocks (2.7% of those investigated). In goats, only one PI animal (0.08%) was detected. Sequence analysis of the 5'-end untranslated region (UTR) revealed that the strains of Border disease virus (BDV) detected were closely related to genotype 3 but the PI animals did not show any clinical signs of Border disease. The goat was PI with bovine viral diarrhoea virus-1 (BVDV-1). On one farm a high abortion rate among sheep had been observed 1year before the study was carried out but the other farms did not show any evidence of reproductive failures. Pestiviruses are endemic in small ruminants in some Alpine regions of Austria and PI healthy animals as described here have a key epidemiological role. A successful BVDV eradication programme in Austria will create highly pestivirus-susceptible cattle populations. Sheep and goats present a high risk for the reintroduction of pestiviruses to cattle herds because they are less likely to be considered to be PI. The results underline the need for the immediate consideration of small ruminants in eradication programmes.