Abstract: To explore the mechanism of inactivation of microorganisms exposed to pulsed electric fields (PEF), protein content, intracellular enzymes and DNA of PEF-treated Saccharomyces cerevisiae cells were investigated by Lowry, SDS-PAGE, APIZYM kit and flow cytometry methods. Results showed that, after PEF treatment, the protein concentration in cells decreased significantly (p<0.05), and the protein bands pattern was smeared with disappearance of bands of both small molecular weight and molecular mass ≥ 60 kD. The activities of all the 13 selected enzymes of S. cerevisiae were reduced in various degrees by PEF treatment. Decreases in DNA content and DNA denaturation were also identified. Therefore, the inactivation of microorganisms treated by PEF was related to the inactivation of intracellular enzymes, the leakage or denaturation of cellular protein and DNA.