Purpose: Gentlefile (GF) is a newly developed stainless steel rotary system claimed to have superior shaping ability compared to nickel-titanium (NiTi) rotary systems. The purpose of this study was to compare the incidence of the canal transportation and centring ability of ProTaper Next (PTN) and GF rotary systems. Methods and materials: Thirty-two mesiobuccal root canals of mandibular molars with an angle of curvature ranging from 25 to 45 degrees were randomly divided into two groups of 16 canals each according to the instrument used for preparation: PTN or GF files. Cone beam computed tomography (CBCT) was used before and after preparation of the samples to assess the amount of canal transportation and centring ability at 3, 6 and 9 mm from the apex. Data were scored and statistically analysed using independent t test. The significance level was set at P ≤ 0.05. Results: The GF system produced more canal transportation than the PTN system at 3 and 6 mm with a statistically significant difference (P ≤ 0.05), whereas at 9 mm there was no statistically significant difference between the two systems (P ≤ 0.05). PTN showed better centring ability than the GF at 6 mm and this difference was statistically significant (P ≤ 0.05). However, at 3 and 9 mm there was no significant difference between the two systems (P ≥ 0.05). Conclusions: Under the limitations of this study both systems produced canal transportation but the PTN system resulted in better root canal preparation with a lesser degree of canal transportation and better centring ability than the GF system.