Purpose: To determine whether variation in glucan synthesis by Streptococcus mutans isolates is associated with caries development in children receiving a fluoride mouth rinse (FMR). Materials and Methods: Of 122 children (aged 9 to 10 years), 64 had received FMR (FMR(+) group) and the remaining 58 children had not (FMR(-) group). The number of decayed and filled teeth (DFT) and increases in the number of DFT in 1 year (dDFT) were recorded. Saliva samples were collected to isolate the clinical S. mutans strains. The isolates were incubated in heart infusion broth supplemented with 1% sucrose, then the amount of water-insoluble glucan (WIG) formed on a glass tube surface was evaluated. Results: In the FMR(-) group, children carrying S. mutans had a higher DFT (P = 0.039) and tended to have a higher dDFT (P = 0.080) than the others. In the FMR(+) group, although the differences between children with and without S. mutans were not significant, children carrying S. mutans that produced a high amount of WIG had higher dDFT than the other S. mutans-positive children (P = 0.034). Conclusions: This study revealed that the variation in glucan synthesis by S. mutans is associated with caries development in children receiving a FMR. Keywords: child, dental caries, glucans, Streptococcus mutans