Electrochemical disinfection is regarded as one of the alternatives to chemical chlorination due to its possibility to generate free chlorine from chloride ions naturally presented in drinking water at low concentration. The inactivation efficiency of electrochemical disinfection system is mostly dependent on many parameters, such as electrode material, cell configuration, electrolyte composition, microorganisms, current density and electrolyte flow rate. The choice of electrode material is one of the most important parameters which affect the efficiency of the whole process. Moreover, the overall design of the system must support simple and rapid production of disinfected water. In this study titanium oxide-based ceramic electrodes TiO2-x, with a high resistance to corrosion and low absorption coefficient were used to construct and demonstrate an automated disinfection system applicable for flow conditions.