This paper presents a new microreactor dedicated for pulsed electric field treatment (PEF), which is a pasteurization method that inactivates microorganisms with short electric pulses. The PEF microreactor consists of a flow-through channel with a constriction where the electric field is focussed. Compared to a laboratory-scale setup 25 times lower voltages were needed to obtain the same electric field strength due to the close electrode spacing. A finite element model showed that the electric field intensity is very homogeneous throughout the channel, which is crucial for the pasteurization processes. Experiments where artificial vesicles, loaded with carboxyfluorescein, were electroporated showed that the maximum transmembrane potential adequately described the processes both in the microreactor and the laboratory-scale setup, although the length scales are different. Electroporation started at a transmembrane potential of 0.5 V, reaching a maximum fraction of electroporated vesicles of 51% at a transmembrane potential of 1.5 V. The partial electroporation is not a result of the heterogenity of the vesicles or the electric field. With this new PEF microreactor it is possible to study the PEF process in more detail. © The Royal Society of Chemistry 2005.