Aims: The aim of the study was to compare the efficacy of 37% phosphoric acid, 12% nitric acid, 17% EDTA in endodontic smear layer removal and degree of erosion in the apical third of endodontic canals. Methods and Material: One hundred and four extracted single-rooted human teeth were randomized into four groups (n = 26) and instrumented using ProTaper Universal Ni-Ti rotary instruments. Each canal was irrigated with one of the following solutions: 37% phosphoric acid, 12% nitric acid, 17% EDTA, 5.25% NaOCl (control). All specimens were then irrigated with 5 mL distilled water and dried with sterile paper points. Kruskal-Wallis and Mann-WhitneyU statistical tests were used. Results: Scanning electron microscopy (SEM) evaluation showed no significant differences among test reagents in smear layer removal. However, the efficacy of 12% nitric acid and 17% EDTA in removing the smear layer was significantly greater than 5.25% NaOCl (control). Degree of erosion could not be evaluated. Conclusion: Protocols used in this study were not sufficient to completely remove the smear layer in the apical third of shaped root canals.