Borna disease virus (BDV) is a neurotropic pathogen that infects a wide variety of vertebrates. We have developed a new electrochemiluminescence immunoassay (ECLIA) for the detection of antibodies to BDV, using three synthetic peptides corresponding to the amino acid residues 3-20 and 338-358 of p40 and 59-79 of p24 peptide of BDV. Using the ECLIA, we examined serum samples for the presence of anti-BDV antibodies in 20 rats (experimentally BDV-infected and uninfected) and 38 horses (13 US horses, experimentally infected and uninfected, and 25 Japanese horses, feral and domestic). The ECLIA, performed in a double-blind manner, detected anti-BDV antibodies in rats with a history of BDV infection, giving results that were in agreement with indirect immunofluorescence assay and/or Western blot (WB) analysis. The ECLIA also correctly identified all three experimentally infected horses and four domestic American horses that were seropositive for BDV antibodies by WB. Among the Japanese horses, at least two out of 10 feral and six out of 15 domestic horses were seropositive for BDV. In most of these cases, the specificity of immunoreactivity was verified by blocking with soluble p40 and p24 peptides.