A model was developed that enables the quantification of thermal and electric field effects during the pulsed electric field (PEF) inactivation of alkaline phosphatase (ALP) and lactoperoxidase (LPO) in milk as well as Escherichia coil in apple juice. The entire PEF process which consisted of pre-heating of the liquid, PEF treatment and rapid cooling to refrigeration temperatures was analyzed with regard to the thermal load to which the product was exposed. Finite volume method (FVM) was used to calculate the heat transfer phenomena within the heating and cooling devices. The temperature increase during PEF treatment due to ohmic heating was calculated using the total specific energy input. A temperature-time profile of the PEF process depending on different treatment conditions was obtained. Heat inactivation kinetics of native ALP and LPO in raw milk and E. coil in apple juice were determined by glass capillary method. A model for the calculation of inactivation levels based on a first order inactivation kinetic was obtained. A MathCad tool was programmed to perform the mathematical comparison of the thermal exposure of ALP, LPO and E. coil during the PEF process and their thermal stability. The impact of different temperature-time profiles resulting from the variation of the PEF treatment parameters on inactivation and residual activity were investigated. The quantification of thermal and electric field effects and their contribution to the overall inactivation revealed that thermal effects were the major reason for the enzyme inactivation and had large impact on the inactivation of E. coil at elevated temperatures. The model may be used for the optimization of a PEF process to achieve the minimization of thermal inactivation of heat-sensitive components but also for the beneficial use of thermal effects to improve the microbial inactivation. (C) 2010 Elsevier Ltd. All rights reserved.