Recently many researches on plaque removal effect and therapeutic effect of toothpaste containing natural medicines are being studied in early periodontal diseases. The purpose of this study is to examine the clinical and microbiological effect of toothpaste containing natural medicines such as camomile, rhatany, myrrh，sage oil, glycyrrhetinic acid and vitamin E. Sixty three subjects with gingivitis were divided into an experimental group which performed normal oral hygiene procedure with toothpaste containing natural medicines and vitamine E and a control group which also performed normal oral hygiene procedure with Syrinmed? toothpaste without containing herbal extracts and vitamine E. At the baseline, 2 weeks, and 4 weeks, subjects were analyzed for clinical study and microbiological study. After 2 weeks and 4 weeks use of their respective toothpastes, statistically significant decreases of gingival index, plaque index, and bleeding index were shown in both the control and the experimental group. The degree of decrease was more significant in the experimental group than the control group. A statistically significant decrease of pocket depth, and gingival crevicular fluid were shown in both the control and lie experimental group. A statistically significant increase of cocci was shown in both the control and the experimental group, the degree of increase was more significant in the experimental group than control group. A statistically significant decrease ofnon-motile rods, and motile rods were shown in both the control and the experimental group, the degree of decrease was more significant in the experimental group than the control group. Spirochetes increased weakly in both the control and the experimental group but a statistic significance was not shown. A statistically significant decrease of anaerobic bacteria, aerobic bacteria, and black pigmented Bacteroides were shown in both the control and the experimental group. These results indicate that the use of toothpaste containing natural medicines is effective in the prevention and the treatment of periodontal diseases.