The aim of this study was to evaluate the effects of herbal medicines in treating periodontal diseases. Three Chinese herbal composites [Conth Su (CS), Chi Tong Ning (CTN) and Xi Gua Shuang (XGS)], widely used for prevention and treatment of periodontal diseases, and the major components of these composites were tested for their ability to: (1) alleviate disease progression of experimental periodontitis in hamsters, (2) inhibit bacterial growth, and (3) induce mutations. Our results indicate that in treating experimental periodontitis, there were no significant differences between the animal groups with or without the use of Chinese herbal medicines in terms of the degree of inflammation, alveolar bone resorption, and rate of repair. However, hamsters treated with CS presented earlier regenerative epithelium. CTN demonstrated superior bacterial inhibition ability among all tested herbs (MIC 0.025 g/ml); CS showed good anti-bacterial abilities at a concentration of 0.05 g/ml. It is interesting to note that while both CS and CTN were capable of inhibiting bacterial growth, none of the individual herb components showed comparable bacterial inhibition abilities. None of the tested herbal composites or their components showed signs of inducing cell mutations using the Ames test. These results indicated that traditional Chinese herbal medicines, which have been used to treat periodontal diseases for hundreds of years by Chinese people, can effectively inhibit bacterial growth without causing cell mutation. Further investigation into their possible clinical applications in periodontal therapy is encouraged.