Background: It is very important to assess the effects of NaOCl and ClO2 on dentine deproteination because these solutions are in contact with dentine during endodontic treatment and may affect the physical and chemical structure of dentine. Objectives: This study aimed to analyze the effects of sodium-hypochlorite (NaOCl) and chlorinedioxide (ClO2) on the chemical structure of human dentine by Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy. Methods: Fifteen human maxillary incisor roots were cut longitudinally into two parallel dentin discs being approximately 4x4x2 mm in size. 30 samples were randomly allocated to 6 groups treated with 5.25% NaOCl or 0.014% ClO2 (1, 5, or 10 minutes); self-control was used. The effect of solutions on the organic and inorganic components of the radicular dentine surface was analyzed using the amide:phosphate ratio and carbonate:phosphate ratio. The intragroup differences (paired t-test) and intergroup differences (one-way analysis of variance and Tukey’s posthoc test) were analyzed. Results: The intragroup comparisons showed the amide:phosphate ratio to be higher at all times at ClO2. NaOCl caused a decrease in the amide:phosphate ratio at 10 minutes (p<0.05). The intergroup comparison showed that NaOCl caused a greater decrease in amide:phosphate at all times compared to ClO2 (p<0.05). All comparisons demonstrated no significant difference in the carbonate: phosphate ratio (p>0.05). Conclusion: Considering the results of this study, it is recommended to avoid prolonged exposure to minimize NaOCl-induced dentine deproteination. It should also be taken into account that ClO2 increases the amide:phosphate ratio in radicular dentine, and this effect is advantageous in clinical use for collagen structure, contrary to the negative impact of NaOCl.