This study evaluated the effect of 2% chlorhexidine digluconate (CHX) used as a therapeutic primer on the long-term bond strengths of two etch-and-rinse adhesives to normal (ND) and caries-affected (CAD) dentin. Forty extracted human molars with coronal carious lesions, surrounded by normal dentin, were selected for this study. The flat surfaces of two types of dentin (ND and CAD) were prepared with a water-cooled high-speed diamond disc, then acid-etched, rinsed and air-dried. In the control groups, the dentin was re-hydrated with distilled water, blot-dried and bonded with a three-step (Scotchbond Multi-Purpose-MP) or two-step (Single Bond 2-SB) etch-and-rinse adhesive. In the experimental groups, the dentin was rehydrated with 2% CHX (60 seconds), blot-dried and bonded with the same adhesives. Resin composite build-ups were made. The specimens were prepared for microtensile bond testing in accordance with the non-trimming technique, then tested either immediately or after six-months storage in artificial saliva. The data were analyzed by ANOVA/Bonferroni tests (alpha = 0.05). CHX did not affect the immediate bond strength to ND or CAD (p > 0.05). CHX treatment significantly lowered the loss of bond strength after six months as seen in the control bonds for ND (p < 0.05), but it did not alter the bond strength of CAD (p > 0.05). The application of MP on CHX-treated ND or CAD produced bonds that did not change over six months of storage.