The purpose of this study was to compare the effect of natural sugar substitutes-stevia, jaggery, and honey on salivary pH and Streptococcus mutans (S. mutans) count in saliva. Children aged between 7 and 12 years with no active carious lesion were selected. A total of 80 subjects were randomly selected and divided into three experimental groups and one control group, with 20 subjects in each group. Prior to rinsing with the respective solutions, the baseline pH and S. mutans count were evaluated for each individual. All solutions were freshly prepared whenever required. After rinsing with the respective solutions, saliva samples were collected to evaluate pH and S. mutans count. The pH was analyzed at different time intervals, that is, 0 (immediately after rinsing), 15, and 30 minutes. The S. mutans count was analyzed after 30 minutes of rinsing with the respective solutions. The results were tabulated and statistically analyzed using one-way analysis of variance (ANOVA) and post hoc tests. The results depicted that group I (stevia) showed a maximum increase in salivary pH, followed by group III (honey) and group III (jaggery) at different time intervals (0, 15, and 30 minutes). The maximum number of subjects who had shown a decrease in S. mutans count were from group III (honey), followed by group I (stevia), and group II (jaggery) after 30 minutes of rinsing with the respective solutions when compared to baseline S. mutans count. It is a universally known fact that dental caries is a multifactorial disease process, one of the key factors of which is the consumption of sugar. Of all the fermentable carbohydrates, sucrose is considered the archcriminal in the carious process. Hence, this advocates the need for developing suitable sugar substitutes that help in controlling dental caries. An ideal sugar substitute should not only minimize the risk of dental caries but also should have nutritional benefits. Natural sugar substitutes (stevia, jaggery, and honey) have the ability to reduce caries risk in children. Sharma W, Bhola M, Bajaj N, et al. Comparative Evaluation of Changes in Salivary pH and Streptococcus mutans Count in Saliva by Natural Sugar Substitutes: An In Vivo Study. Int J Clin Pediatr Dent 2023;16(5):728-733.