It has been reported that the adhesive resin layer of all-in-one adhesives is permeable and allows the formation of a water channel or water tree. The effects of a smear layer on the ultra-structure of bonding interface created with three all-in-one adhesives and a resin composite were evaluated in this study. Dentin surface was ground with of 180-, 600-, or 2000-grit SiC paper to produce different smear layer thickness. The bonding interfaces were observed under a transmission electron microscope without demineralization. Voids of various sizes and water channels were found at the bottom of the adhesive resin layer along the bonding interface of SiC 180-grit dentin, while SiC 2000-grit dentin did not produce any voids. The results showed that the voids were possibly related to water that had penetrated from the underlying dentin. A smear layer may have an adverse influence on the bonding performance of all-in-one adhesives to dentin.