In order to study the application of antibodies against recombinant proteins for detecting Borna disease virus (BDV) phosphoprotein (p24) and nucleoprotein (p40) (BDV‑p24/p40) on paraffin sections by immunohistochemistry. The purified fusion p24 and p40 proteins were used for the preparation of polyclonal and monoclonal anti‑p24 and anti‑40 antibodies， which were confirmed by ELISA and western blotting. Paraffin sections were made from BDV‑infected Sprague‑Dawley (SD) rats (n=20)， PBS‑injected SD rats (n=20)， normal SD rats (n=20) and normal C57 mice (n=20). Immunohistochemical staining was performed according to the EnVision™ two‑step protocol. Heat‑mediated antigen retrieval was performed using the retrieval buffer sodium citrate (1 mM; pH 6.0). All the antibodies against recombinant proteins exhibited good sensitivity and specificity. There were significant differences between the BDV‑infected group and the BDV‑uninfected group for poly‑ and monoclonal anti‑p24 and ‑p40 antibodies. These antibodies against recombinant proteins may be used effectively to detect BDV p24 and p40 in paraffin sections.