BACKGROUND Saline irrigations are routinely employed during endoscopic sinus surgery to remove mucous and debris from the sinus cavities. What is unknown is whether this results in a quantitative reduction in pathologic bacteria within the sinus mucosa. The objectives of this study were to quantify the amount of 5 different bacteria (Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa, coagulase-negative Staphylococcus (CNS), and Streptococcus pneumoniae) within the maxillary sinus and to determine the impact of saline irrigations on bacterial counts. METHODS Twenty patients with chronic rhinosinusitis were prospectively enrolled. After bilateral maxillary antrostomies, biopsies were taken of the maxillary sinus mucosa prior to any irrigation. In each patient, the left maxillary sinus was then irrigated with 250 cc of normal saline (NS) with a pressurized pulse-irrigation device and the right side was irrigated with 250 cc of NS using a 30-cc syringe attached to a curved suction tip. Repeat maxillary sinus mucosal biopsies were then taken from each side. Each biopsy was analyzed using quantitative polymerase chain reaction to determine the presence and amount of each of the bacteria. RESULTS Saline irrigations were found to significantly reduce the amount of S. aureus, P. aeruginosa, and S. pneumoniae found within the maxillary sinus mucosa. No difference was found for H. influenzae or CNS. No difference in bacterial load reduction was able to be shown between the pressurized saline flushes and manual saline rinse methods. CONCLUSION Intraoperative saline irrigations are able to significantly reduce the amount of potentially pathogenic bacteria within the diseased sinus mucosa.