Background: The aim of this pilot study was to evaluate the effects of mouthrinses containing 7.5% povidone iodine and 0.2% chlorhexidine on bacteraemia following impacted third molar surgery. Methods: Thirty-four patients were enrolled in this study. Patients in the first group were asked to rinse their mouth with the mouthrinse containing 7.5% povidone iodine, patients in the second group were asked to rinse with the mouthrinse containing 0.2% chlorhexidine and patients in the third group were asked to rinse with 0.9% NaCl (sterile saline) solution. All rinses were used for one minute preoperatively. Peripheral venous blood samples were collected at baseline (preoperatively), 1 and 15 minutes after the completion of surgical tooth removal. Each blood sample was divided in two, placed in aerobic and anaerobic culture bottles and processed for microbiological examination. Results: Bactaeremia was detected in 33% of the povidone iodine group, 33% of the chlorhexidine group and 50% of the control group. Isolated bacteria were 58% anaerobes and predominantly 92%Streptococcus species. Incidence of bacteraemia was reduced with chlorhexidine and povidone iodine mouthrinses in third molar surgery, although the difference was not statistically significant (p > 0.05). Conclusions: Bacteraemia was reduced with antibacterial mouthrinses in third molar surgery. The results of this study should be confirmed with further studies conducted on a larger patient population and with different antibacterial mouthrinses.