The aims were to evaluate the levels of bacterial species in saliva and in situ and to assess whether the design of brackets influences the risk of developing periodontal disease. Twenty patients (13.3 mean age) were bonded with self-ligating brackets and a conventional bracket. Saliva was collected before bonding and 30 and 60 days after bonding. One sample of each bracket was removed 30 and 60 days after bonding. The analysis was determined by checkerboard DNA-DNA hybridization. The data was evaluated by the non-parametric test. A significant increase in the levels of bacterial species in the saliva occurred in 15 of the 22 analyzed species. The self-ligating brackets presented the highest incidence percentages for the orange and red complexes 60 days after bonding. In situ analyses showed different patterns according to the bracket design. The levels of Campylobacter rectus showed significant differences (p = 0.011) 60 days after bonding among the three brackets; the highest values were observed in the In-OvationA (R) R bracket. The bracket design seems to influence the levels of bacterial species involved in periodontal disease. Considering the wide variety of bacterial species, additional studies are needed to aid in the establishment of effective protocols to prevent the development of periodontal disease during orthodontic treatment. A dynamic alteration in the oral microbiota may lead to inflammatory reactions in the supporting soft and hard tissues. The different types of brackets interfere with bacterial adherence. Bracket design should be considered in orthodontic treatment.