Materials and methods. In this clinical trial, 120 12-14 year-old students were selected and divided into three groups. Each group was given one of fluoride, chlorhexidine, or fluoride-chlorhexidine mouthwashes. They were asked to use it twice a day for two weeks. Salivary samples were collected at baseline and after two weeks. Data were analyzed by Wilcoxon and Kruskal-Wallis tests. 

Results. In all the study groups, there were statistically significant reductions in salivary S. mutans counts two weeks after using the mouthwashes (P < 0.05). In addition, fluoride-chlorhexidine mouthwash had a significant effect on the reduction of S. mutans count in comparison with fluoride alone. The prevalence of oral side effects in fluoride-chlorhexidine mouthwash was more than 90%. 

Conclusion. Adding fluoride to chlorhexidine mouthwash can significantly decrease salivary S. mutans count after two weeks. Fluoride-chlorhexidine has the highest rate of oral side effects between the evaluated mouthwash compounds.