Objectives: This study evaluated the influence of chlorhexidine (CHX) on the microtensile bonds strength (${mu}TBS$) of resin core with two adhesive systems to dentin in endodontic cavities. Materials and Methods: Flat dentinal surfaces in 40 molar endodontic cavities were treated with self-etch adhesive system, Contax (DMG) and total-etch adhesive system, Adper Single Bond 2 (3M ESPE) after the following surface treatments: (1) Priming only (Contax), (2) CHX for 15 sec + rinsing + priming (Contax), (3) Etching with priming (Adper Single Bond 2), (4) Etching + CHX for 15 sec + rinsing + priming (Adper Single Bond 2). Resin composite build-ups were made with LuxaCore (DMG) using a bulk method and polymerized for 40 sec. For each condition, half of specimens were submitted to ${mu}TBS$ after 24 hr storage and half of them were submitted to thermocycling of 10,000 cycles between $5^{circ}C$ and $55^{circ}C$ before testing. The data were analyzed using ANOVA and independent t-test at a significance level of 95%. Results: CHX pre-treatment did not affect the bond strength of specimens tested at the immediate testing period, regardless of dentin surface treatments. However, after 10,000 thermocycling, all groups showed reduced bond strength. The amount of reduction was greater in groups without CHX treatments than groups with CHX treatment. These characteristics were the same in both self-etch adhesive system and total-etch adhesive system. Conclusions: 2% CHX application for 15 sec proved to alleviate the decrease of bond strength of dentin bonding systems. No significant difference was shown in ${mu}TBS$ between total-etching system and self-etching system.