Background: Bacterial plaques are the important etiologic factors of gingival (periodontal) diseases. It is well established that orthodontic appliances (bracket, band and arch wire) playing an important role in growth of these plaques, therefor periodontal diseases the main problems of orthodontists and these patients. Recognition of etiologic factors of these diseases is important for prophylaxis and cure performances, and the aim of present study was evaluation of clinical and microbial of gingival infections in patients treated with fixed orthodontic appliances. Materials and Methods : By refer to the orthodontic department of three dentistry clinics of Karaj city, 65 patients under fixed orthodontic treatment were selected and at third and twelfth month of treatment, after clinical parameters evaluation such as gingival index, bleeding on probing and probing depth, microbiological sampling was performed from subgingival plaques of these patients. Whole genomic DNA of the samples was extracted using a kit, and a 16S rRNA gene segment-based multiplex PCR method was used to simultaneous detection of Aggrigatibacter actinomycetemcomtans and Porphyromans gingivalis. Results: Molecular evaluation of this study showed that Aggrigatibacter actinomycetemcomtans was not present in tested samples, although transient changes in Porphyromans gingivalis frequency was reported (%20.1±0.41 (T3) and %2.7±0.16 (T12) P=0.02) , also clinical evaluation revealed appearance of signs of moderate gingivitis and stability of the inflammatory lesion until termination of treatment in these patients. Conclusion: Present study showed that was no meaningful relationship between Porphyromans gingivalis and Aggrigatibacter actinomycetemcomitans to increase of chronic gingivitis in treated patients with fixed orthodontic appliances, and this long term therapy did not to prepare patients into periodontitis.