Introduction: The aim of this study was to evaluate the effects of self-ligating brackets and conventional brackets ligated with stainless steel ligatures on dental plaque retention and microbial flora. Methods: Twenty boys (mean age, 14.2 ± 1.5 years) underwent bonding with self-ligating bracket systems and conventional standard edgewise bracket systems ligated with stainless steel ligatures with a split-mouth design. Clinical measurements, including plaque index, probing pocket depth, and bleeding on probing, were obtained before bonding, 1 week after bonding, and 3 months after bonding. Supragingival plaque samples were obtained at baseline and 3 months after bonding for the detection of bacteria. A quantitative analysis for Streptococcus mutans, Streptococcus sobrinus, Lactobacillus casei, and Lactobacillus acidophilus was performed using real-time polymerase chain reaction. The Mann-Whitney U test and the Hotelling T2 multivariate test were used for statistical comparisons of the groups. Results: The numbers of S mutans, S sobrinus, L casei, and L acidophilus were not statistically different between self-ligating brackets and conventional brackets ligated with stainless steel ligatures (P >0.05). The 2 archwire ligation techniques showed no statistically significant differences in plaque index, bleeding on probing, and probing pocket depth values of the bonded teeth (P >0.05). All clinical parameters and the numbers of all microorganisms showed statistically significant increases from baseline to 3 months after bonding in both groups (P <0.001). Conclusions: Self-ligating brackets and conventional brackets ligated with stainless steel ligatures do not differ with regard to dental plaque retention. Copyright © 2013 by the American Association of Orthodontists.