AimTo compare the effect of autoclave cycles on the surface topography and roughness of HyFlex CM and HyFlex EDM instruments using atomic force microscopy (AFM) analysis.MethodologyEight new files of each brand were subdivided into four subgroups (n=2/each subgroup). One group was allocated as the control group and not subjected to autoclave sterilization. The other three groups were subjected to different numbers (1, 5, and 10) of autoclave sterilization cycles. After the cycle instruments were subjected to AFM analysis. Roughness average (Ra) and the root mean square (RMS) values were chosen to investigate the surface features of endodontic files. The data was analyzed using one-way ANOVA and post hoc Tamhane tests at 5% significant level.ResultsThe lowest Ra and RMS values were observed in the HyFlex EDM files that served as the control and in those subjected to a single cycle of autoclave sterilization (P<0.05). The highest Ra and RMS values were observed in the HyFlex CM and HyFlex EDM files that were subjected to 10cycles of autoclave sterilization (P<0.05). The surface roughness values of the HyFlex CM group showed a significant increase after ten autoclave cycles, whereas those of the HyFlex EDM group exhibited a significant change after five autoclave cycles (P<0.05).ConclusionsAlthough the initial surface roughness values of the HyFlex EDM files were lower than those of the HyFlex CM files, the surface roughness values of the EDM files showed a statistically significant increase after 5cycles of autoclave sterilization. In contrast, the surface roughness values of the HyFlex CM files did not increase until 10cycles of autoclave sterilization.Clinical relevancePresent study indicated that autoclave sterilization negatively affected the surface roughness of the tested NiTi files.