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Background Despite of the rapid development in the field of dental adhesives, the issue of reduction in dentin bond durability has still not been resolved. The activity of dentinal endogenous enzymes such as MMPs is one of the most important causes of failure in resin composite restorations. The aim of this study was to investigate the influence of Chlorhexidine on micro-tensile bond strength of two types of commercially available self-etch adhesives. Material and Methods Twenty four sound and freshly extracted molars were selected. Four standardized flat mid-coronal dentinal disks were prepared from each tooth. The specimens were randomly assigned to 6 groups (n=16). Groups A(control group) and B were treated with Clearfill SE Bond based on the manufacturer's instructions. Groups C and D were treated with 2% Chlorhexidine 60 seconds before applying Clearfill SE Bond. Groups E and F were treated with Peak Universal Bond according to the manufacturer's instructions. All groups were stored in distilled water in room temperature. Microtensile bond strength in groups A, C, and E were tested 24 hours after preparation, while microtensile bond strength in groups B, D, and F were tested after 3 months storage and 3000 thermal cycles(5-55 °C). Statistical analysis was performed with SPSS 20 and µTBS test results were analyzed using the Two-way ANOVA test. Results µTBS was not significantly different between groups A, C, and E after 24 hours (P>0.5). There was no significant difference between groups B (Clearfill SE Bond + Aging) and D (Clearfill SE Bond + 2% CHX + Aging). The Peak Universal µTBS significantly decreased after the aging procedure (P