The presence of Borna disease virus (BDV)-specific RNA was traced by the reverse transcriptase-polymerase chain reaction in conjunctival fluid, nasal secretions and saliva of horses which were seropositive but did not have any history of clinical Borna disease. Positive reactions encompassed sequences encoding the p24 BDV-specific protein. Virus specificity of the amplified product was confirmed by hybridization with the respective oligomer probe. Viral infectivity or virus-specific antigen was not found in any of these secretions by conventional assays in cell culture and immunoblotting.