This study evaluated the effect of a 2% chlorhexidine-based disinfectant (CHX) on the short-term resin-dentin bond strength of a self-etch adhesive system to human dentin with different mineral contents. Dentinal mineralization was tested at 4 levels (sound, and after 2, 4, or 8 days of demineralization-remineralization cycles) and disinfectant at 2 levels [deionized water (DW, negative control) and CHX]. Dentin demineralization induced by pH-cycling was characterized by cross-sectional hardness (CSH). Each dentin surface was divided into halves, one treated with DW and the other with CHX (5 minutes). Each surface was bonded with a self-etch adhesive system and restored. The specimens were sectioned and subjected to microtensile bond testing. CSH and microtensile bond strength (µTBS) data were analyzed by regression analysis and ANOVA-Tukey tests (α = 5%), respectively. The groups treated with CHX resulted in mean µTBS similar to those found for the groups in which the dentin was exposed to DW (p = 0.821). However, mean µTBS were strongly influenced by dentin mineralization (p < 0.05): the bond strength found for sound dentin was lower than that found for dentin cycled for 8 days, which was even lower than the bond strengths for dentin cycled for 2 or 4 days. The results suggest that the degree of dentin demineralization affects the bond strength of self-etching adhesives, but the use of CHX does not modify this effect.