To evaluate the microtensile bond strength of self-etching adhesive systems in dentin treated with 2% chlorhexidine digluconate (CHX). The occlusal surfaces of 20 human molars were removed and divided into eight groups: 1A, Clearfil SE adhesive (SE) with self-etching technique (TS); 1B, SE with TS and previous application of CHX; 2A, Scotchbond Universal (SBU) adhesive with TS; 2B, SBU adhesive with TS and previous application of CHX; 1C, SE with total-etching technique (TT); 1D, SE with TT and previous application of CHX; 2C, SBU with TT; 2D SBU with TT and previous application of CHX. Composite resin (5mm) was applied on the hybridized surface. Samples were subjected to microtensile test and evaluated on Scanning Electron Microscope (SEM) and with energy-dispersive X-ray (EDX). Low values of bond strength were observed in groups 1A (39,77±11,56) and 2A (40,84±12,49) comparing with 1B (22,86±5,18) and 2B (27,02±5,58). TS group presented adhesive type remover fracture while TT groups presented cohesive at the top of hybrid layer. EDX revealed the presence of CHX crystals for TS, which was not found in the TT. The previous application of chlorhexidine on dentin decreased the bond strength of adhesive systems on self-etching technique.