(1) Background: Root canal preparation constitutes an important factor for success in endodontics. However, various complications may occur during this stage. The aim of this study was to compare the incidence of cracks within radicular dentin after instrumentation with ProTaper Next (PTN), WaveOne Gold (WOG), and Twisted Files (TF), which utilize different kinematics. (2) Methods: Eighty single-rooted teeth were classified into four groups (n = 20). Three groups were instrumented using PTN (X1, X2), WOG (Primary), and TF (SM1–3). The non-instrumented group constituted the control group. Post-preparation, the roots were sectioned 3, 6, and 9 mm from the apex using a low-speed saw (Southbay Technology Inc., San Clemente, CA, USA). The specimens were viewed through a microscope at x25 magnification (Leica M320, Wetzlar, Germany), and their surface was assessed tactilely to determine the presence of the crack. (3) Results: Partial cracks within radicular dentine were observed in all study groups (PTN: n = 4/20%, WOG: n = 3/15%, TF: n = 4/20%); no cracks were observed in the control group. No significant differences were observed among experimental groups. OR values for the incidence of cracks were: OR = 11.182 for PTN, OR = 8.2 for WOG, and OR = 8.2 for TF. (4) Conclusions: Instrumentation with PTN, WOG, and TF may result in dentinal cracks formation.