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Abstract Background: Studies with cetylpyridinium chloride (CPC) mouth rinses that range from 1 use to 6 months of use have documented the clinical efficacy of these formulations on supragingival plaque and gingivitis. Objective : The objective of the present study was to compare the effects of a commercially available mouth rinse containing 0.05% CPC versus a fluoride mouth rinse on the anaerobic bacteria found in dental plaque. Antimicrobial effects on the organisms of the supragingival plaque, a natural biofilm, were determined after 1 use and after 14 days of use of each mouth rinse. Methods : After enrollment, adult subjects from China completed a 1-week washout period and provided baseline samples of supragingival plaque for analysis of anaerobic bacteria. Subjects were randomly assigned to receive a commercially available mouth rinse formulated with 0.05% CPC or a fluoride mouth rinse. Subjects were assigned to each group according to a computer-generated randomization sequence. They were instructed to rinse with 20 mL of either the CPC or the fluoride mouth rinse for 30 seconds. Microbiologic analyses of dental plaque samples were conducted 12 hours after the first use of assigned mouth rinse. Subjects were instructed to continue twice-daily rinsing with their assigned mouth rinse for the next 14 days in addition to brushing their teeth with a commercial fluoride toothpaste. Dental plaque samples for microbiologic analyses were collected on day 15; this was done 12 hours after the final use of the assigned mouth rinses. A dentist conducted oral examinations before each sample collection to evaluate hard and soft tissue health over the course of the study. Results : The study included 117 adults (62 females, mean age, 28.70 years; 55 males, mean age, 30.41 years). Subjects rinsing with the CPC mouthwash (n = 58; mean age, 29.41 years) reported significant reductions in anaerobic bacteria versus those issued the fluoride rinse (n = 59; mean age, 29.61 years) 12 hours after 1 use and 12 hours after 14 days of use ( P < 0.001). The mean percent reduction in anaerobic bacteria between the CPC mouth rinse and the fluoride mouth rinse was 29.98% after 1 use and 57.90% after 14 days of use. All enrolled subjects completed the study without any adverse events. Conclusion : Use of the CPC mouth rinse was associated with significant reductions in the anaerobic bacteria of supragingival plaque compared with fluoride mouth rinse use in these adult subjects.