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The study aimed to compare the canal transportation and centring ability of M two R (Mt), Neoniti (Nn) and WaveOne Gold (Wg) systems during retreatment procedure using Cone Beam Computed Tomography. Forty freshly extracted single-rooted mandibular premolars were selected. Teeth were decoronated and were standardized to a length of 15mm from the root apex. The root canals were instrumented using Protaper rotary files. All the teeth were embedded in soft putty blocks, and post-instrumentation Cone Beam Computed Tomography (CBCT) imaging was done at 3, 6 and 9 mm levels. Root canals of all the specimens were obturated with gutta-percha using AH Plus sealer. Samples were randomly divided into four groups (n = 10), and retreatment in each group was performed as follows: Group I - using Hand instrumentation (Hi), Group II- using Mtwo R (Mt), Group III - using Neoniti (Nn), Group IV- using WaveOne Gold (Wg). CBCT imaging of all the teeth was repeated after the completion of retreatment procedures at the same position. The centring ability and canal transportation were calculated at 3, 6, and 9 mm from the apex in mesiodistal and buccolingual directions. Statistical analysis was performed using ANOVA and Post Hoc Tukey tests. Results have shown a significant difference for canal transportation mesiodistally at 9 mm from the apex (P< 0.05), where Hi removed more dentin in one direction compared to Wg. A significant difference in centring ability was observed buccolingually at 9 mm from the apex (P< 0.05), where Hi was less centred in the canal compared with Nn and Wg. Among the tested file systems Mt, Nn, Wg, there was no significant difference in canal transportation and centring ability during retreatment at 3, 6, and 9mm from the apex in both dimensions.