Previous seroepidemiological and molecular epidemiological studies of Borna disease virus (BDV) showed considerably high rates of infection in horses, cattle, cats, and humans in Hokkaido, Japan. Here, we further demonstrate high rates of specific antibodies to BDV and BDV RNA in peripheral blood mononuclear cells (PBMCs) from healthy sheep bred on the same island. The BDV prevalences by immunoblotting and/or reverse transcriptase PCR were 0% (0 of 19) in newborns (<1 month old), 51.7% (15 of 29) in lambs (1 to 6 months old), and 36.7% (11 of 30) in adults (>2 years old). Among animals positive for BDV, 60% of lambs and 45.5% of adults contained BDV RNA in PBMCs while 46.7% of lambs and 90.9% of adults contained specific antibodies to BDV. Thus, it is suggested that virus replication in the blood, as observed in lambs, is usually reduced in adulthood by raising immune responses to BDV.