Introduction: Despite advances in adhesive dentistry, lasting bonds between indirect restorations and dentin remain a challenge. Objective: Therefore, the aim of this study was to evaluate the effect of chlorhexidine on the bond strength of self-adhesive cements to dentin after storage for 24 h and 90 days. Material and methods: Forty-eight human third molars crowns were included in polyvinyl chloride matrices using acrylic resin and worn to expose a flat dentin area. The specimens were randomly distributed into 8 groups (n = 12) in accordance with the self-adhesive cement (Rely X U200 and Smart Cem 2), the dentin treatment (application or not of 2 % chlorhexidine digluconate solution for 1 min) and the storage period (24 h or 90 d). Two cylinders' cements (1.4 x 1 mm) were constructed on the dentin surfaces of each sample, stored in distilled water for 24 h or 90 days and submitted to a micro-shear test. Subsequently, a failure analysis was performed to classify the failure into adhesive, cohesive, and mixed. Data were subjected to ANOVA and Tukey (0.05) tests. Results: There was a statistically significant difference between the materials (Rely X U200 > Smart Cem 2 -p < 0.05) regardless of the surface treatment and the storage period. Conclusion: The chlorhexidine application did not affect the immediate or delayed bond strength values, regardless of the self-adhesive cement.