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Aim Restorative dentists employ different bonding systems between the resin and the dentin and other dentinal tissues to achieve the goal of micromechanical retention. Studies have shown that the bond between composite and dentin degrades over time because of the action of matrix metalloproteinases (MMPs) on collagen fibrils left unprotected by acid etching. The MMPs may be partially responsible for hybrid layer degradation. Since chlorhexidine (CHX) inhibits MMPs, we hypothesized that CHX would decelerate the loss of resin-dentin bonds. Hence, this in vitro study is intended to evaluate the effects of 2% CHX on hybrid layer and bonding interface. Materials and methods Totally, 40 freshly extracted molars were randomly divided into four experimental groups. In all 40 specimens, class II cavities were prepared to a depth of 1 mm below the dentinoenamel junction with no axial wall, but the elimination of the proximal enamel ridge. The teeth were then randomly divided into four experimental groups, i.e., All Bond 2 without 2% CHX (group I), All Bond 2 with 2% CHX (group II), One Coat 7.0 without 2% CHX (group III), and One Coat 7.0 with 2% CHX (group IV). All the specimens were derooted and sectioned mesiodistally into two halves and placed under water at 37°C for 3 months and observed under scanning electron microscope for the hybrid layer and resin tag formation. Results Groups I and II showed statistically significant difference when the presence/absence of resin tags was compared. When groups III and IV were compared for the presence/absence of hybrid layer and resin tags, the results were statistically significant. Conclusion Between all the four experimental groups, irrespective of the bonding systems used, we concluded that groups with 2% CHX usage showed promising results with presence/ absence of hybrid layer and resin tags formation. Clinical significance Studies suggest that the bond between composite and dentin degrades over time because of the action of MMPs on collagen fibrils left unprotected by acid etching. Measures should be taken to prevent this from happening and thus allow bond between composite and dentin last longer.