AIM: To assess the impact of the rotary file systems Protaper Gold and Hyflex EDM on the apical foramen of mandibular molars. Materials and method: The study included 10 mandibular molars with a total of twenty mesial root canals. Access cavities were set up, and the working length at the apical foramen was determined. Protaper Gold (PTG) and Hyflex EDM were used in Group 1 and Group 2, respectively, for biomechanical preparation of the canals (n=10). It was instrumented up to file size #25/0.06. AF areas (A0, A1) were evaluated under 10X magnification both before and after instrumentation. Each canal's foraminal distortion was computed by deducting A1 from A0. Results: In all instances, apical foraminal distortion was visible. Compared to Protaper Gold, Hyflex EDM system displayed the least amount of AF deformation. The amount of deformation that is produced may be significantly influenced by the alloy, taper and cross-section of the file.