To investigate the antimicrobial activities and effect of grapefruit seed extract(GFSE) on the physiological function of microorganism, antimicrobial activity, fatty acids of bacterial cell lipid and amino acids of bacterial cell protein were measured. The change of cell morphotype was observed by transmission electron microscope. GFSE was very stable on the wide range temperture and pH. The growth rate of E. coli and B. suvtilis were decreased above 40ppm GFSE There fore, minimum inhibitory concentration (MIC) of the E. coli and B. subtilis to GFSE were determined around 40ppm. In the change of fatty acids quantities, hexadecanoate was significantly decreased on the treatment compared with control in case of E. coli, whereas tridecanoate was not detected in case of B. subtilis. In the change of amino acids quantities, alanine, glutamic acid, glycine, lysine were decreased on the treatment compared with control in case of E. coli and B. subtilis Transmission electron microsgraphs(TEM) showed the microbial cells were destroyed by GFSE.