Purpose: The objective of this study was to compare engine-driven instrumentation methods in relation to the appearance of defects in the walls of the root canal. Materials and methods: In total, 60 single-rooted human teeth, extracted for periodontal reasons, were conserved in Deltalab Eurotubo sterile A with 2% thymol until use. The teeth were decoronated and randomly divided into three groups (n = 20). In Group 1, canal negotiation was achieved with a size 10 K-file, followed by rotary pre-instrumentation with Pathfiles. Instrumentation with the ProTaper Universal system was carried through to a final file F4. In Group 2, the teeth were instrumented with the WaveOne Gold system according to the manufacturer's instructions. In Group 3, the teeth were left unprepared as control. After this, the canals were irrigated with 2 ml of distilled water and the teeth were conserved in distilled water. The samples were sectioned transversely before subsequent analysis on three levels. Defects were scored: 0 for no defects, 1 for cracks. Results: Reciprocating instrumentation with the WaveOne Gold Large instrument reduced by 30% the frequency of occurrence of cracks in the root canal walls in the coronal and apical thirds with respect to ProTaper F4 instrumentation (P 0.05). There were no statistically significant differences between the systems in the incidence of cracks in the middle third. Conclusions: Instrumentation with WaveOne Gold generated fewer cracks in the coronal and apical thirds of the root canal compared with the ProTaper system. Keywords: cracks, ProTaper Universal, WaveOne Gold