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Background The aim of this study was to assess the root morphology of mandibular molar teeth using cone‑beam computed tomography (CBCT) in patients with periodontal disease. Methods In total, 88 patients were included in this study (70 patients with periodontitis and 18 patients with non-periodontitis). This cross-sectional study involved CBCT images taken for patients who visited the dental clinic of Imam Abdulrahman Bin Faisal University (IAU) from January 2019 to March 2021. The following data were analyzed on the mandibular molars: root length, number of root canals, root trunk, distance between roots, accessory canals in the furcation area (ACF), bone loss, and furcation involvement. Results The mesial root was longer than the distal root in the mandibular molars of periodontitis and non-periodontitis patients. A statistically significant difference was observed between non-periodontitis and periodontitis patients regarding the number of mesial root canals of the mandibular first molar; 70% had two root canals in non-periodontitis patients, compared with 86.1% in periodontitis patients (p = 0.04). First molars of non-periodontitis patients had significantly longer root trunks than periodontitis patients (4.65 ± 0.90 compared with 4.09 ± 1.02, p = 0.007). There was a statistically significant difference in bone loss between non-periodontitis and periodontitis patients (0% and 25% for first molars, and 2.8% and 23.6% for second molars, respectively). Accessory furcation canals were 2.9 % in second molars and 7.1 % in first molars in periodontitis patients, which were higher compared with non-periodontitis patients. Conclusions The first molar showed a longer root trunk in non-periodontitis patients than in periodontitis patients. The mean mesial and distal root lengths were also greater in the first than the second molar. Accessory canals in the furcation area were more observed in first molars than in second molars in periodontitis patients compared with non-periodontitis patients., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2021, Madi et al.)