Real-time reverse transcriptase-polymerase chain reaction (real-time RT PCR) and capture IgM and IgG enzyme-linked immunosorbent assay (ELISA) are routinely recommend for diagnosis of Japanese encephalitis virus (JEV) infection. Recent, gold nanoparticles have been demonstrated to improve the efficiency of PCR by its excellent heat transfer property. Quantum dots have been used for molecular imaging of disease diagnosis. The goal of this study is to apply gold nanoparticles and quantum dots for enhancing the efficiency of molecular and immunological diagnostics on the JEV infection. Gold nanoparticles improved sensitivity of E gene-specific application using PCR systems, showing that addition of 5nM or 10nM gold nanoparticles shortens PCR cycles from 35 to 25 cycles. Addition of 5nM and 10 nM gold nanoparticles increased the efficiency of the real-time PCR by 5.39 to 7.08 and 7.06 to 8.17 cycles, respectively. Addition of 5nM and 10 nM gold nanoparticles increased the efficiency of the real-time RT-PCR by 2.77 to 5.39 and 3.95 to 6.18 cycles, respectively. In addition, gold nanoparticle conjugated JEV envelope (E)-specific scFv antibody that was identified from phage display random scFv antibody libraries was used to develop the immunological assay of JEV diagnostics. Moreover, quantum dot conjugated (E)-specific scFv antibody was applied for In vivo molecular and cellular imaging of the JEV infection.