This study focused on adhesive interface morphologic characterization and nanoleakage expression of resin cements bonded to human dentin pretreated with 1% chlorhexidine (CHX). Thirty-two non-carious human third molars were ground flat to expose superficial dentin. Resin composite blocks were luted to the exposed dentin using one conventional (RelyX ARC) and one self-adhesive resin cement (RelyX U100), with/without CHX pretreatment. Four groups (n = 8) were obtained: control groups (ARC and U100); experimental groups (ARC/CHX and U100/CHX) were pretreated with 1% CHX prior to the luting process. After storage in water for 24 h, the bonded teeth were sectioned into 0.9 × 0.9 mm(2) sticks producing a minimum of 12 sticks per tooth. Four sticks from each tooth were prepared for hybrid layer evaluation by scanning electron microscope analysis. The remaining sticks were immersed in silver nitrate for 24 h for either nanoleakage evaluation along the bonded interfaces or after rupture. Nanoleakage samples were carbon coated and examined using backscattered electron mode. Well-established hybrid layers were observed in the groups luted with RelyX ARC. Nanoleakage evaluation revealed increase nanoleakage in groups treated with CHX for both resin cements. Group U100/CHX exhibited the most pronouncing nanoleakage expression along with porous zones adjacent to the CHX pretreated dentin. The results suggest a possible incompatibility between CHX and RelyX U100 that raises the concern that the use of CHX with self-adhesive cements may adversely affect resin-dentin bond.