Glutaraldehyde is used as a disinfectant for endoscopes, but is an irritant and so should be replaced by an alternative. Electrolysed acid water (EAW) has a bactericidal effect, and an endoscopic washing device using EAW has been developed in Japan. To investigate the effect of EAW on the infectivity of viruses, we treated duck hepatitis B virus (DHBV), which has similar properties to hepatitis B virus, with EAW, and determined the number of remaining infectious virus particles in a bioassay system. One-day-old Pekin ducks were inoculated with duck serum containing 105.5 ID50 DHBV; the serum had previously been incubated with 100 volumes of EAW or ion-exchanged water at room temperature for 7 min. DHBV infection was indicated by detection of viral DNA in duck serum samples 1–8 weeks after inoculation. Treatment of serum with EAW diminished DHBV infectivity whereas treatment with ion-exchanged water did not. The virus load was estimated to have been reduced to 101–103 ID50 during the first 1 min and to <100.5 ID50 in the next 6 min of incubation when compared with the control. Thus, EAW directly inactivates DHBV and its clinical application is recommended.