The effects of both the electric and flow parameters on the lethality and energy efficiency of a pulsed electric fields (PEF) treatment were studied. An experimental plan was designed in order to study the microbial inactivation of Saccharomyces cerevisiae and Escherichia coli cells inoculated in a buffer solution. The following process parameters were taken into consideration: electric field strength (13-30 kV/cm), total specific energy input (20-110 J/mL), flow rate of the processed stream (1-4 L/h) and number of passes through the chamber (up to 5). The results showed that, at a fixed flow rate (2 L/h), microbial inactivation of both microbial strains increased with increasing field strength and applied energy input. The maximum inactivation level (5.9 Log-cycles for S. cerevisiae and 7.0 Log-cycles for E. coli) corresponded to the more intensive PEF treatment (30 kV/cm and 110 J/mL). However, for any given field strength applied, the inactivation rate decreased by increasing the energy input. This behavior was attributed to the presence of heterogeneous treatment conditions due, for example, to a different morphology (size and shape) or cell membrane (composition, structure), a local variation of the electric field strength in the treatment chamber, the tendency of microbial cells to form clusters, or a non-uniform distribution of the residence time of the product in the PEF chamber. A more effective stirring of the microbial suspensions which was achieved, at a fixed field strength (18 kV/cm), either by increasing the flow rate with a single pass operation through the PEF chamber, or by operating in re-circulating mode at a constant flow rate, provided a significant increase in the effectiveness and energy efficiency of the pulse treatment. A mathematical model based on the Weibull distribution adequately described the inactivation kinetics of both microbial strains under different flow dynamic conditions. (C) 2011 Elsevier Ltd. All rights reserved.