Background: It is very important to assess the effects of NaOCl and ClO<inf>2</inf> 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% ClO<inf>2</inf> (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 ClO<inf>2</inf>. 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 ClO<inf>2</inf> (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 ClO<inf>2</inf> 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.