Background: Chlorhexidine could have effect on shear bond strength of composite resin-dentin. Objective: The purpose of this study is to compare two methods of chlorhexidine application of shear bond strength degradation between composite resin and dentin. Methods: Thirty samples of dentin were taken from the crown of premolars and then divided into three groups (n = 10). Group 1 were applied bonding without chlorhexidine, group 2 were applied with liquid chlorhexidine and followed by bonding, group 3 were applied bonding which contains chlorhexidine. Each group was divided into two subgroups (n = 5): the group with and without 10% NaOCl immersion for one hour. Then, 4 samples in each subgroup were used to measure shear bond strength using Universal Testing Machine, and 1 sample was examined with Scanning Electron Microscope (SEM). Data were analyzed using SPSS 17 by Mann-Whitney and Kruskal Wallis test. Results: The highest mean shear bond strength without 10% NaOCl immersion was in group 1, while the highest mean with 10% NaOCl immersion was in group 3. Significant differences occurred between the groups 1 and 2, groups 2 and 3. Conclusion: Method of using bonding contains chlorhexidine can increase and inhibit degradation shear bond strength between composite resin and dentin.