If it is to be effective, preventive dental treatment must be based on an individual’s risk of caries and periodontal disease. However, hitherto, preventive treatment has been generally conducted without proper caries-risk assessment because of lack of knowledge about an individual’s caries risk. This study sought to identify high-risk adult patients and examine the effectiveness of preventive programs. Data for 442 patients from a single general practice who met the inclusion criteria were analyzed. Multiple logistic-regression analysis showed that high levels of mutans streptococci (SM) correlated with the onset of primary and secondary caries, with odds ratios of 2.34 (95%CI: 1.15-4.76, p = 0.019) and 2.22 (95%CI: 1.06-4.62, p = 0.034), respectively. Lactobacilli (LB) also correlated with secondary caries, with an odds ratio of 3.34 (95%CI: 1.35-6.85, p = 0.007). When the patients were checked after three years of a preventive program, the correlation with SM and LB disappeared. Survival analyses by Cox regression models and Kaplan-Meier methods showed that secondary caries was difficult to control by conventional preventive programs alone in patients with high levels of cariogenic bacteria. In conclusion, cariogenic bacteria play an important role in the incidence of caries, and additional intensive preventive treatment should be considered for high-risk patients.