Remaining root dentin thickness plays a key role in the longevity of endodontically treated teeth. Purpose: The aim of this study was to compare the root canal wall thickness in the danger zones of mandibular incisors before and after their instrumentation with two different NiTi rotary systems by means of CBCT. Methodology: Thirty lower incisors of patients aged 45 – 55 years underwent primary endodontic treatment with two NiTi files systems: ProTaper Universal and WaveOne Gold. The changes of the root canal thickness in the danger zones of the incisors were investigated by two CBCT scans – one at the beginning of the experiment and the other after the shaping of the root canals. Results: Shaping of the root canals of lower incisors with the two NiTi systems significantly decreased the mesio-distal root dentin thickness in all root canal levels when compared with the baseline values (p≤0.001). NiTi files from both experimental groups removed substantially more root dentin in the coronal portion of the root than in the apical (p<0.05). The intergroup comparison between the two tested NiTi systems revealed no statistically significant difference in their performance at the three observation levels (p>0.05). Conclusions: Both NiTi systems performed equally and removed dentin more aggressively in the coronal portion of the root. Further clinical experiments are necessary to find the minimally invasive endodontic systems for an optimal preservation of root dentin in the danger zones of mandibular incisors.