Statement of Problem: Fixed orthodontic appliances are considered to be a clinical risk factor in terms of gingival and enamel integrity, because of plaque accumulation around the bracket bases which increases the levels of microorganisms. Although chlorohexidine significantly reduces plaque accumulation, but its side effects prevents its common use.Purpose: The purpose of this in vivo study was to compare the antibacterial effects of two herbal mouthwashes of persica and matrica with chlorhexidine in fixed orthodontic patients.Materials and Methods: A total of 68 orthodontic patients of 13-19 years old (who referred to a private clinic in 2002) with good oral hygiene were randomized into 4 groups. Group 1 (control) used water, group 2 used Chlorhexidine, group 3 used Persica and group 4 used matrica, twice a day for 3 weeks. The number of all bacterial colonies around the ring elastics of the upper canine and premolar growing in the culture media were counted before (T1) immediately after (T2) and 3 weeks after (T3) the use of the mouthwashes and water in all 4 groups and analyzed.Results: Chlorhexidine, Persica and Matrica mouthwashes significantly reduced the amount of bacteria around the brackets immediately and after 20 days after their use. The intergroup comparison showed that persica and matrica at T2 and T3 had significant differences with chlorhexidine group. So, Chlorhexidine was the most effective antibacterial mouthwash in T2 and T3. Persica and Matrica groups showed no significant differences both in T2 and T3, but had significant difference with the control group.Conclusion: The use of herbal mouthwashes such as Persica and Matrica in orthodontic patients can significantly reduce the amount of microorganisms around the bracket bases without any side effect such as tooth discoloration which is seen with Chlorhexidine.Key words: Mouthwash, Chlorhexidine, Persica, Matrica