The aim of this ex vivo study was to evaluate the effect of using a patency file on apical transportation and curve straightening during canal instrumentation with the ProTaper rotary system. Seventy permanent mandibular first molars with mesiobuccal canals, measuring 18–23 mm in length and with a 25–40° curvature (according to the Schneider method), were selected. The working lengths were determined and the teeth were mounted and divided into two experimental groups: (A) prepared by the ProTaper system without using a patency file (n = 35) and (B) prepared by the ProTaper system using a patency file (n = 35). Radiographs taken before and after the preparation were imported into Photoshop software and the apical transportation, and curve straightening were measured. Data were analyzed using independent t‐test. Partial correlation analysis was performed to evaluate the relationship between the initial curvature, transportation, and curve straightening (α = 0.05). Using a patency file during canal preparation significantly decreased both apical transportation and curve straightening (P < 0.001). There were significant relationships between the angle of curvature, transportation and curve straightening in pairs (P < 0.001). Apical patency is recommended during root canal preparation with the ProTaper rotary system.