It is believed that Borna disease virus (BDV), an etiological agent of progressive polioencephalomyelitis in horses and sheep, is closely associated with psychiatric disorders in humans since the prevalence of BDV is higher in psychiatric patients than in blood donors. We investigated whether or not BDVs in humans are derived from infected domestic animals, by characterizing the BDVs in blood donors and horses derived from the same region of Hokkaido island, Japan. The seroprevalences (2.6 to 14.8%) of BDV were significantly higher in the blood donors from four regions where most horse farms are concentrated, compared with only 1% in the blood donors from Sapporo, the largest city in Hokkaido.BDV RNA was also detected in peripheral blood mononuclear cells from most of the seropositive horses and blood donors by nested reverse transcriptase-polymerase chain reaction. These findings support that BDV may be horizontally transmitted, at least in part, from infected horses to humans.