Objectives: To evaluate the quality of hybrid layer through assessment of nanoleakage at resin composite/dentin interface following sonic application of self-etch adhesives. Methods: The occlusal surfaces of 120 molars were ground flat until superficial dentin was exposed. Two types of self-etch adhesives were applied inactively, manually and sonically. After light curing, resin composite was packed incrementally and light cured. Half of the specimens were thermocycled between 5 and 550C ± 20C for 500 cycles. Specimens were immersed in ammoniacal silver nitrate solution for 24 hours and exposed to photodeveloping solution for 8 hours. The specimens were observed under Environmental Scanning Electron Microscope using backscattered electron mode. Data were submitted to one way ANOVA, three way ANOVA and student t test. Results: Sonic application of non-thermocycled one step self-etch adhesive specimens showed the least nanoleakage values, while inactive application of the thermocycled one step self-etch adhesive specimens showed the highest nanoleakage values. Conclusions: Increase in manipulative steps of self-etch adhesive systems has resulted in an increase in nanoleakage at resin composite/dentin interface. Nanoleakage at resin composite/dentin interface is reduced after effective agitation of the self-etch adhesive systems irrespective of their application techniques. Thermocycling of resin composite restorations adversely affect the marginal integrity which is more pronounced with one-step self-etch adhesive systems.