Background The aim of the present investigation was to evaluate and compare the efficacy of frequently used chemical agents in terms of their capacity to eliminate the smear layer after instrumentation, as observed via scanning electron microscopy (SEM). Materials and methods Sixty extracted single-rooted mandibular premolar teeth, each with roots 15 mm in length, were used in this study. The teeth were divided into one control group and four study groups, each containing 12 teeth. In Control Group 0, teeth were irrigated with 3 ml of saline only. In Group 1, teeth were irrigated initially with 3% sodium hypochlorite (NaOCl) and then given a final rinse with 3 ml of 17% ethylenediaminetetraacetic acid (EDTA) for one minute. In Group 2, teeth were irrigated with 3% NaOCl and given a final rinse with 3 ml of a mixture of tetracycline, acid, and detergent (MTAD, BIOPURE) for one minute. In Group 3, teeth were irrigated with saline and given a final rinse with 3 ml of 17% EDTA for one minute. In Group 4, teeth were irrigated with saline and given a final rinse with 3 ml of MTAD for one minute.One-half of each tooth was chosen and prepared for scanning electron microscopic (SEM) examination at the cervical, middle, and apical thirds. These were observed at magnifications of up to 1,000 times to check for the presence or absence of a smear layer. The data were analyzed using the Kruskal-Wallis test and post-hoc Dunn's test. Results All of the root canal irrigation protocols exhibited superior efficacy compared to the control group in the elimination of the smear layer. Group 2 (3% NaOCl with MTAD) showed the lowest mean scores, compared to all the groups, followed by Group 1 (3% NaOCl with 17% EDTA). MTAD was more effective than EDTA. The smear layer was effectively removed from the apical third, followed by the middle and coronal thirds of the root. Conclusion Initial irrigation with 3% NaOCl and one-minute final irrigation with 3 ml MTADwas the most effective root irrigant, and particularly indicated in teeth with infection of the apical third.