Objective: The purpose of this study was to compare a manually operated preparation system such as ProTaper manual file and its counterpart engine-driven rotary instrument regarding the transportation of standardized simulated root canals. Materials and methods: Forty resin-simulated root canals were filled with ink, and pre-instrumentation images were acquired using a stereomicroscope. Samples were divided into two groups according to the instrument's operation mode. Preparation was performed using ProTaper manual or rotary up to size F2. Pre- and post-instrumentation images were obtained and superimposed for measurement at eight different measuring points (0 to 7 mm from apex). Results: There were no significant differences between the groups at levels 0, 2, 3 or 7 mm. At levels 1, 4, 5 and 6 mm, engine-driven mode with rotary ProTaper instrumentation promoted higher canal transportation than manually operated mode using ProTaper manual (P 0.05). In both groups, the pronounced canal transportation occurred at level 5 mm. Conclusions: Both operation modes caused deviation in simulated standardized root canals; however, the manually operated system with ProTaper manual files generated significantly less deviation than the motor-driven mode using rotary ProTaper instruments. Keywords: canal transportation, centring ability, curved canal, ProTaper