Objectives This study aimed to assess the effect of using chlorhexidine (CHX)-releasing elastomeric ligatures on the number of Streptococcus mutans (S. mutans) in the saliva and dental plaque and on elastomeric ligatures in orthodontic patients. Materials and Methods: This double-blind clinical trial evaluated 30 orthodontic patients between 14 to 25 years, who were randomly divided into two groups. CHX-releasing elastomeric ligatures were used in the test group while the conventional elastomeric ligatures were used for the control group. Saliva samples were collected at baseline, and 7, 14, 21 and 28 days after the intervention. Plaque samples were also collected at baseline and after 28 days. Elastomeric ligatures were collected in both groups after 28 days. The collected samples were cultured to count the number of S. mutans. Data were analyzed using the MannWhitney and Wilcoxon tests. Results: The salivary count of S. mutans was significantly lower in the test group at 7, 14, 21 and 28 days (P<0.05). The S. mutans count on the surface of CHX-releasing ligatures was significantly lower than that on the surface of conventional ligatures (P<0.05). However, no significant difference was noted in S. mutans count in plaque samples between the two groups (P>0.05). The salivary level of S. mutans significantly decreased during the course of study in the test group. Conclusion: CHX-releasing elastomeric ligatures can significantly decrease the salivary count of S. mutans in orthodontic patients.