Aim The purpose of this study was to clarify the mechanism of the antibacterial action of two high potential and natural food additives, epigallocatechin gallate (EGCg) and theaflavin-3,3 '-digallate (TF3), on Clostridium perfringens. Methods and Results Minimal inhibitory concentrations were determined by the serial dilution method. Afterwards, the cells were treated with 250 or 1000 mg l(-1) of EGCg and 125 or 500 mg l(-1) of TF3 and morphological changes were observed and cell sizes were also measured under fluorescence microscopy. Our results showed that TF3 had a twice stronger antibacterial activity than EGCg against C. perfringens. Phase-contrast and fluorescence microscopy confirmed that the bacterial cells elongated without DNA segregation and septum formation in the presence of 250 mg l(-1) EGCg. While in the higher concentration of EGCg and TF3, cell growth was suppressed. Bacterial cells reached to around 12 mu m after the 24 h incubation with 250 mg l(-1) EGCg, but the cells were shorter than the control at 1000 mg l(-1) of EGCg. After washing and incubating the elongated cells in fresh medium, DNA segregated at 2 h of incubation. The average cell length decreased gradually and reached the normal size at 8 h. Conclusion It seems that EGCg at a low concentration affected the proteins involved in the septum formation, DNA segregation and cell division. Furthermore, the high concentration of EGCg and TF3 seemed to cause stronger cellular damage to C. perfringens. Significance and Impact of the Study These polyphenols are widely distributed in all higher plants especially in tea plants, and people tend to use natural food additives rather than synthetic ones. EGCg and TF3, as natural food additives, can prevent C. perfringens food poisoning along with other potential health benefits.