The purpose of this study was to apply Scutellariae radix extract herbal medicine to dental practice and to investigate the effects of Scutellariae radix extract on dental caries. After adding Scutellaria radix 500 g to 70% methanol, extraction was done for 3 h, and the extract was filtered and then lyophilized. This study was conducted after obtaining the approval of the IRB of Inje University (No. 2-1041024-AB-N-01 - 20140514-HR-055-04; approval date: 2014-08-27). Among the patients who visited M Dental Clinic located in Busan, South Korea from January 2015 to January 2016, and who did not have any systemic disease, 180 patients were included in this study after excluding those with incomplete data. The subjects were divided into the 0.9% saline (JW Pharmaceutical) gargling group (60 persons), the 0.005% chlorhexidine (Bukwang Pharm) gargling group (60 persons), and the 10% Scutellaria radix gargling group (60 persons). Before gargling, the patients’ simplified oral hygiene index (S-OHI), dental caries activity test value, and amount of coccus were measured. After gargling with 15 ml gargling solution for 1 min, the subjects were instructed to spit saliva for 1 min to completely remove the gargling solution, without leaving any residue, and then the variables were measured again. The study results showed that the S-OHI, Alban test value, and amount of stretococcus mutans (S. mutans) decreased in all the groups compared to before gargling. In the comparison of the three groups, however, no significant differences were found in the S-OHI, Alban test value, and amount of S. mutans before gargling (P>0.005) while significant differences were found in the S-OHI and Alban test value after gargling (P<0.005). It is believed that the use of the natural extract Scutellaria radix for gargling instead of chlorhexidine, which contains chemical ingredients with side effects, will enable safe and effective oral management.