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To compare the effect of 5.25% NaOCl or 17% EDTA solutions on the surface topography and roughness of GTX, TF, RaCe and Hero Shaper instruments using atomic force microscopy (AFM) analysis.Four new files of each brand were subjected to AMF analysis; then each group was subdivided into two subgroups (n = 2) in which instruments were immersed in either 5.25% NaOCl or 17% EDTA solutions for 5 min, thereafter subjected to AFM analysis again. Ra and the RMS values were chosen to investigate the surface features of endodontic files.Before immersion in irrigating solution, TF and Hero Shaper instruments had the significantly highest roughness values and RaCe had the significantly lowest values (P ≤ 0.05). After immersion in NaOCl, GTX and RaCe instruments were not significantly different from the new instruments, nor between them. There was a significant increase in Ra and RMS values for TF and Hero Shaper instruments over that of untreated ones and that of GTX and RaCe instruments. No significant increase in surface roughness of the instruments was recorded with EDTA.17% EDTA did not significantly affect the surface roughness of the instruments, whilst 5.25% NaOCl increased the surface roughness of TF and Hero Shaper significantly more than that of RaCe and GTX instruments.