Background: The aim of the study is to compare the effect of various bracket ligation systems and ceramic brackets with metal brackets on periodontal status in the patients undergoing orthodontic treatment that will be quantified in terms of plaque index ,gingival index, probing pocket depth at different time intervals of treatment along with a quantitative analysis of various microorganisms implicated to be most commonly present in dental plaque in patients undergoing orthodontic therapy using real time PCR. Materials & methods: Twenty patients seeking orthodontic treatment visiting the Department of Orthodontics were included in this study. All the subjects were informed about the procedures to be performed and signed informed consent was obtained from the parent/guardian. Patients were instructed to maintain their normal dietary habits and report back to the department after 3 weeks. The patients were randomly divided into two study groups. Each group consisting of ten patients. In Group I, self-ligating metallic brackets were compared with conventional metallic brackets. In Group II, self-ligating ceramic brackets were compared with conventional ceramic brackets. This comparison is carried out using split mouth study in which one type of bracket is used in maxillary right and mandibular left quadrant and the other type of brackets on maxillary left and mandibular right quadrant. Patients are recalled after 3 weeks and a clinical periodontal evaluation of patients is done in terms of plaque index, probing pocket depth and bleeding on probing before the bonding procedure was performed. The values were measured for all the teeth that are bonded except for the molars. All the teeth were evaluated at four sites per tooth ( distofacial ,facial, mesiofacial and lingual). The clinical evaluation is followed by bonding using standardized isolation taking care that there should be no bonding agent left over anywhere around the bracket base. Results: Comparison of four types of brackets for S. mutans using PCR revealing that the increase in S mutans count among different bracket systems as statistically not significant (p value =0.5091). Comparison of four types of brackets for S. sobrinus using PCR revealing that the increase in S.sobrinus count among different bracket systems as statistically not significant (p value =0.5795). Comparison of four types of brackets for L.acidophillus using PCR revealing that the increase in L. acidophillus count among different bracket systems as statistically not significant (p value =0.2023). Comparison of four types of brackets for L.casei using PCR revealing that the increase in L. casei count among different bracket systems as statistically not significant (p value =0.7922). Conclusion: The microbiological counts for self ligating ceramic brackets was almost the same as conventional ceramic brackets Intra bracket comparison at different time intervals revealed a significant increase in bacterial count as well as the periodontal index for all the brackets. Key words: Brackets, Orthodontic, Plaque