Objective: It is important to sterilize oral cavity with antibacterial agent before surgery for preventing infection. The object of this study was to compare the effect on reduction of salivary bacterial counts according to applied time when povidone-iodine (PVI) and chlorhexidine gluconate (CHX), most broadly used materials in dentistry, were applied intraorally before the surgery. Methods: Sixty subjects were divided into 6 groups. PVI and CHX were applied in each group for 1, 2 and 3 minutes, respectively. Then salivary microbacteria taken before and after applying the materials were cultured using 5% sheep blood agar plate. Results: There was significant difference in reduction of microbacteria in both PVI and CHX and the effect did not show differences depending on time. When applied for a minute, PVI showed somewhat higher reduction rate than CHX, but in the other groups, there was no difference in reduction rate. Conclusion: We found that there was no significant difference in sterilization ability of PVI and CHX in all groups in this study. Therefore, both agents would get sufficient effect when applied for a minute.