BACKGROUND White spot lesions (WSLs) are a common complication after orthodontic treatment. The aim of this study was to characterize and compare the antimicrobial properties of selenium-containing vs. fluoride-containing orthodontic materials. MATERIAL AND METHODS Antibacterial efficacy of orthodontic materials (SeLECT Defense bonding agent, Adhesive agent, Band Cement, Transbond Plus SEP bonding agent, Transbond Plus Adhesive agent, Fuji I Band cement, Fuji Ortho LC Adhesive agent, Ortho Solo Bonding agent, Transbond XT bonding agent, and Transbond XT primer) was tested with the inhibition of 2 bacterial strains: S. mutans (ATCC 10449) and L. acidophilus (ATCC 4356). The antimicrobial efficacy of the materials was measured by agar diffusion test. The diameters of inhibition zones around each disk were measured in millimeters (mm). RESULTS Materials containing selenium and fluoride showed significant differences from the negative control (both p<0.001). Orthodontic materials containing fluoride as a potential antimicrobial agent showed larger zones of inhibition in total (9.1±2.6 mm), the selenium group was the second-most effective (4.7±4.9 mm), and the group without any potential antimicrobial agent showed the least antimicrobial effect (0.9±1.0 mm). Materials from the group with no antibacterial agent were not significantly different from the negative control group (p>0.05). CONCLUSIONS Materials containing selenium carried the most significance when comparing microorganisms with the agent, since they were the only ones showing difference between the 2 microorganisms. They showed statistically significant difference in efficacy against S. mutans, and poor antimicrobial effect against L. acidophilus. These data suggest that orthodontic materials containing selenium might have the potential to prevent WSLs due to their antimicrobial properties.