The purpose of this study was to evaluate the effects of a fluoride mouth-rinsing program (FMR) on dental health after the FMR program was completed. The state of dental health, including caries prevalence, was examined under blind recording conditions concerning participation in the FMR for 11th grade students in 10 public high schools, from 11 municipalities in Niigata Prefecture. The procedures of the FMR were carried out in these areas weekly, with 0.2% NaF, or daily, with 0.05% NaF, supervised by the classroom teachers in each school. The subjects, 321 in total, were classified into 3 rinse groups, each of which participated in the FMR for different periods of time, and a control group. The results of the statistical analysis showed increasing benefits in relation to increasing periods of participation. The reduction rate of caries prevention was the highest in the F11-group, subjects who participated in the program for 11 years from 4 to 14years of age. The F11-group was 56.0% lower in the mean DMFT and 81.8% lower in the mean number of highly progressed carious teeth than the control group, with statistical significance in both cases. The percentage of students who had toothaches or who were absent from school in order to visit a dentist was lower in the rinse groups than in the control group. We conclude that, in countries such as in Japan where caries prevalence is relatively high, a school-based FMR program throughout the school years is profoundly effective in preventing the occurrence and the progression of caries, and it could be the foundation of lifelong dental health care.