Objective: The aim of this study was to investigate the effects of two bonding systems, with and without antibacterial monomers, on marginal bacterial and dye leakage. Materials and Methods: Class V cavities were prepared in extracted teeth for a bacterial leakage test, and the teeth were sterilized using a steam autoclave. Four cavities were not restored for the controls, and the other teeth were divided into two groups (n = 16 cavities each): Clearfil Protect Bond group (CPB) and Clearfil SE Bond group (CSE). After application of the bonding agent, the cavities were restored using a composite resin (Clearfil AP-X). The teeth were thermocycled, stored in a broth culture of 1.56 × 108 colony forming units (CFU)/ml of Streptococcus mutans at 37°C for 10 days, and subsequently processed for bacterial staining. Sections from the demineralized teeth were evaluated under a light microscope. In the dye leakage test, the cavities were restored as described in the bacterial penetration test. After thermocycling, the teeth were immersed in 5% basic fuchsin for 24 h, and then divided in half and observed under a stereomicroscope. The data were analyzed using the Kruskal-Wallis and Mann-Whitney U-tests (P = 0.05). Results: The bacterial stain was detected at the cavity wall of five cavities in both bonding systems. Additionally, two cavities in the CSE group, one cavity in the CPB group, and all control cavities showed bacterial staining within the cut dentinal tubules. Dye staining at the axial cavity wall was detected in only three of the teeth for both bonding systems. Conclusion: The bonding systems used in this study provided an acceptable marginal seal to prevent bacterial and dye leakage. © 2014 Dental Investigations Society.