Background and aims. Streptococcus mutans is the main pathogenic agent involved in dental caries, and may be eliminated using mouthwashes. The objective of this study was to compare the effects of fluoride, chlorhexidine, and fluoride-chlorhexidine mouthwashes on salivary S. mutans count after two weeks of use and determine the prevalence of their side effects on the oral mucosa. 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 mouth-wash 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.