Inactivation of alkaline phosphatase by HTST pasteurization or of lactoperoxidase by high heat treatments is the principal indicator of the efficacy of these treatments to milk (Walstra et al. 2006). Therefore inactivation of alkaline phosphatase and other enzymes (i.e., plasmin peroxidase, microbial proteases and lipases) by PEF treatment has been tested in many studies (Elez-Martinez and Martin-Belloso 2007, Sampedro et al. 2005). Application of 2.2 kV mm electric field strength caused the inactivation of alkaline phosphatase up to 60% in raw milk (Castro et al. 2001). Although results about the effects of electric fields on proteins especially on enzymes are controversial, generally they include the association or dissociation of functional groups, movements of charged chains, and changes in alignment of helices (Tsong and Astunian 1986) For example, alkaline phosphatase molecules treated by PEF at 22.3 kV cm i electric field strength with 0.78 ms pulse width tended to associate and aggregate. It was reported that the polarization created by electrical of dipoles on the enzyme could cause the aggregate formation. The polarization leading to the aggregation of the enzyme was proposed as the mechanism of the inactivation of alkaline phosphatase by et al