Introduction: Modifying the durability of resin bonding systems resulted in introducing materials with cross-link property, such as chlorhexidine (CHX) that can promote the strength of resin-dentin bonding. The aim of this study was evaluation of the effect of CHX on shear bond strength (SBS) of self-etch (SE) and etch-and-rinse (E&R) bonding systems to the primary teeth dentin. Materials and methods: In this in vitro study, 40 freshly extracted primary molars collected and were cut mesiodistally, and then the buccal and lingual surface enamel was grounded. The specimens were randomly divided into two groups: I: Single Bond adhesive and II: Clearfil SE Bond adhesive. Then, each group was divided into two subgroups: On the buccal surface of each sample CHX was applied for 30 seconds and on the lingual surface of (I2, II2 groups), CHX was not applied. The SBS (MPa) of samples was assessed using the Zwick universal testing machine. Data were analyzed by paired t-test and independent t-test using Statistical Package for the Social Sciences (SPSS), version 16. Results: The mean SBS was significantly higher in the Single Bond group with CHX (66.45 ± 8.3) than without CHX (25.43 ± 12.94) in the nonaging group (p = 0.002). There was no significant difference in the mean SBS in the Clearfil SE Bond group with CHX and without CHX in the aging and nonaging groups. Conclusion: CHX had positive influence on immediate SBS of Single Bond adhesive to primary teeth dentin. In addition, no positive effect has been seen in the Clearfil SE Bond system. Clinical significance: Now more researches are needed about the recommendation of CHX in resin restorations of primary teeth. Keywords: Chlorhexidine, Etch-and-rinse adhesive, Failure pattern, Self-etch adhesive, Shear bond strength.