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Perioperative oral care can reduce the risk of postoperative infections. This study examined 1) changes in oral bacteria counts during the perioperative period and 2) differences in bacteria counts in patients with or without endotracheal intubation. 47 patients who visited our hospital dental clinic prior to cardiac valve surgery were prospectively recruited. The number of bacteria on the tongue, tooth surface, and buccal vestibule was measured on the day before and 1, 4, and 7 days after surgery. Oral bacteria counts were statistically compared among time points and between intubation and extubation statuses. The oral bacteria counts on the tooth surface and buccal vestibule significantly increased from the day before surgery to 1 day after surgery, and then decreased from 1 to 4 days after surgery. On the day after surgery, the bacteria counts on the tooth surface and buccal vestibule were significantly higher in the intubated compared with the extubated group. Our findings suggest that the oral bacteria count is elevated just after surgery, especially if the patient has endotracheal intubation, which may increase the risk of aspiration pneumonia. These results highlight the importance of perioperative oral care to prevent postoperative pneumonia.