Background: Many studies have reported risk factors for tooth loss. Oral health instruction is considered effective at improving oral health behavior and oral health. However, few studies have examined the relationship of dental clinic factors, such as the number of dental hygienists and implementation of oral health instructions, with tooth loss. Here, we conducted a multilevel analysis to clarify the dental clinic risk factors associated with tooth loss. Methods: Baseline surveys were conducted at 1216 dental clinics in 46 prefectures in Japan, and 12,399 dental patients aged 20 years and over underwent oral examinations and completed a questionnaire. The dental clinics also completed a questionnaire at baseline. A 3-year follow-up survey included 2488 patients in 585 dental clinics. Multilevel multivariate logistic regression analysis was used to examine the risk of tooth loss at the patient and clinic levels. Results: Of the patient variables, older age, higher mean probing pocket depth, current or past smoking, and bleeding during tooth brushing were associated with higher risks of tooth loss. Individuals with many teeth who visited dental clinics for maintenance were at significantly lower risk of tooth loss. Of the clinic variables, patients attending dental clinics with four or more dental hygienists had a significantly lower risk of tooth loss (OR 0.68, 95% CI 0.50–0.99). Patients attending dental clinics that provide oral health instructions for 20 min or more had a significantly lower risk of tooth loss (OR 0.69, 95% CI 0.50–0.96). Conclusions: In addition to individual risk factors for tooth loss, dental clinic factors such as length of oral health instruction and number of dental hygienists are associated with tooth loss. In dental clinics, ensuring sufficient time for dental hygienists to provide oral health instructions can help prevent tooth loss in dental patients.
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