This study aimed to determine whether the long-term use of a fluoride mouthrinse affects the salivary levels of mutans streptococci. Two hundred and fifteen schoolchildren (aged 9-10 years) participated. One hundred and forty-nine of these children had used a fluoride mouthrinse since 5 years of age at nursery school, and the remaining 66 children had not. DFT (decayed and filled teeth) was recorded, and the salivary levels of Streptococcus mutans and Streptococcus sobrinus were measured using mitis salivarius bacitracin agar. The group that had used a fluoride mouthrinse had a significantly lower prevalence of both S. mutans and S. sobrinus (p = 0.038) and a significantly lower DFT score (p < 0.001) than the other group. Using logistic regression analysis including caries experience at baseline as a dependent variable, the odds ratio of carrying S. mutans alone was 8.0 (p = 0.066) and that of carrying both S. mutans and S. sobrinus was 16.5 (p = 0.022) in the group that had not used the fluoride mouthrinse. Children carrying both S. mutans and S. sobrinus had a higher caries incidence in 1 year than the others, with odds ratios of 5.73 (p = 0.067) in the group with a fluoride mouthrinse and 3.47 (p = 0.035) in the group without it. These results show that the long-term use of a fluoride mouthrinse is associated with reduced salivary levels of mutans streptococci and this bacterial reduction may partly contribute to the suppression of dental caries in children using a long-term fluoride mouthrinse.