Aims: The aim of the present study is to evaluate the effect of cavity disinfection with 2% chlorhexidine (CHX) and Ag-Au nanoparticles on microleakage and resin tag penetrability of composite restoration under in vitro conditions. Materials and methods: Twenty-five human permanent molars extracted for therapeutic reasons were used in the study. Class V cavity of standard dimension was prepared on the buccal and lingual surfaces of the teeth. The teeth were randomly allocated into two groups based on the cavity disinfectant used; group I being 2% chlorhexidine gluconate (chlorhexidine FGM) and group II being cavity disinfectant containing Ag-Au nanoparticles (nanocare gold). In both the groups, the dentin was etched with 37% phosphoric acid and cavity disinfectants were applied following which dentine bonding agent and composite resin were applied and cured. The specimens were then viewed under stereomicroscope and scanning electron microscope for evaluation of microleakage and resin tag formation, respectively. Results: The results were statistically analyzed using independent ‘t’ test. No significant difference was seen between the two groups with respect to the microleakage and resin tag penetration values (p > 0.05). Conclusion: Cavity disinfectant containing Ag-Au nanoparticles had no effect on the sealing ability and resin tag penetrability of composite resin in permanent molars when compared with 2% CHX. Clinical significance: Use of Cavity disinfectant containing Ag-Au nanoparticles with etch and rinse system can be preferred as it satisfies the ideal property of a cavity disinfectant which includes excellent antimicrobial action and non-detrimental effect on the sealing ability and resin tag penetrability.