The effect of chlorhexidine on bond durability of universal adhesives is not clear. The aim of this study was to evaluate the effect of chlorhexidine on 6-month water storage bond strength of adhesive systems. 72 freshly sound human extracted molars were selected. In each tooth both buccal and lingual sides were prepared by bur to reach superficial dentin and randomly divided into 6 groups and 12 sub-groups and bonded with Scotchbond Universal (SBU) or Scotchbond Multi-purpose (SBMP) with/without chlorhexidine (CHX) usage. Group 1: SBU, group2: SBU+CHX, group3: Etch+SBU, group4: Etch+CHX+SBU, group5: Etch+SBMP, group6: Etch+CHX+SBMP. After composite curing, water storage and thermocycling was done. Each group was divided into two subgroups. One was tested immediately, and the other was thermocycled for 5000 cycles (5-55 °C) (it was equivalent to 6 months of storage in distilled water). Shear bond strength test was done and failure modes were determined by Stereomicroscope. The data were analyzed by one-way ANOVA, Tukey post-hoc test and Paired Two test with P<0.050 as the level of significance. Shear bond strength in late SBU (Self etch) was significantly lower than late SBU [Etch and rinse (ER)], P value= 0.0001, also shear bond strength in late SBU [self-etch (SE)] was significantly lower than immediate SBU (SE), P value= 0.01. There were no significant differences between other sub-groups and conditions. The most failure mode was adhesive in all the groups. Long term bonding durability of SBU(ER) was better than SBU (SE). CHX usage had prevented bond strength decrease in SBU and SBMP in long term. CHX usage did not have any effect on immediate shear bond strength of SBU and SBMP. Immediate and late shear bond strength of SBMP with/without CHX usage was similar to SBU(SE, ER).