The electrochemical advanced oxidation process (EAOP) with diamond electrodes may serve as an additional technology to the currently approved methods for water disinfection. Only few data exist on the microbicidal effect of the EAOP. The aim of our study was to investigate the microbicidal effect of a flow-through oxidation cell with diamond electrodes, using Pseudomonas aeruginosa as the test organism. Without electrical current the EAOP had no measurable effect on investigated microbiological and chemical parameters. For direct electrical current a stronger impact was observed at low flow rate than at higher flow rate. Depending on the contact time of the oxidants and the type of quenching reagent added, inactivation of P. aeruginosa was in the range log 1.6-3.6 at the higher flow rate and log 2.4-4.4 at the lower rate. Direct electrical current showed a stronger microbicidal effect than alternating current (maximum reduction log 4.0 and log 2.9, respectively). The microbiological results of experiments with this EAOP prototype revealed higher standard deviations than expected, based on our experience with standard water disinfection methods. Safe use of an EAOP system requires operating parameters to be defined and used accurately, and thus specific monitoring tests must be developed.