Nickel-titanium (NiTi) instruments used to treat root canal infections are affected by autoclave sterilization in various ways. The aim of this study was to compare the effect of autoclave sterilization on two NiTi rotary instruments that undergo different manufacturing treatments: The electro-polished Race and the heat-treated Race Evo, using scanning electron microscope analysis. In this in-vitro study, Race and Race-Evo instruments were subjected to a number of autoclaving cycles (0, 1, 3, 5, and 10). Scanning electron microscopy images were obtained at 3 mm from the tip of the file at 450x and 1000x magnifications. Surface roughness parameters were measured using ImageJ software. The results showed that autoclave sterilization caused a significant decrease in conventional NiTi Race surface roughness. While in Race Evo, surface roughness increased following the first autoclaving cycle. After 10 autoclaving cycles, surface roughness significantly decreased for both Race and Race Evo files.