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The aim of this study was to investigate the effect of the cavity thickness and smear layer on apical sealing ability of mineral trioxide aggregate (MTA) as a root-end filling material.Seventy single-rooted maxillary central teeth were used in this study. All teeth were instrumented to size 50 using a step-back technique. The selected teeth were randomly divided into 4 groups, each containing 15 experimental samples and 5 positive and 5 negative control samples. In the first and second groups (smear+), the teeth were irrigated with only 5.25% NaOCl. In the third and fourth groups (smear−), the teeth were irrigated with 17% EDTA and 5.25% NaOCl to remove the smear layer. Also, in the first and third groups, cavities were prepared as 3 mm. In the second and fourth groups, cavities were prepared as 5 mm. All the root-end cavities were then filled with MTA. Nail varnish was applied to all external root surfaces to the level of the resected root-ends to prevent lateral microleakage. Samples were sterilized in an ethylene oxide sterilizer for 12 hours. The apical 3–4 mm of the roots were immersed in brain heart infusion culture medium with phenol red indicator within culture chambers. The coronal access of each specimen was inoculated every 48 hours with a suspension of Enterococcus faecalis. Bacterial leakage was monitored every 24 hours for 4 weeks. The data obtained were analyzed using a chi-squared test, with α = .05 as the level for statistical significance.There were no statistically significant differences in rate of bacterial leakage among the experimental groups at 1–4 weeks (P > .05). Also, there was no difference between the groups when the 2 thickness groups were combined (P > .05). However, there was statistically significant differences when the 2 smear groups were combined for 4-week observation periods (P < .05). Removal of the smear layer caused significantly more apical microleakage than when the smear layer was left intact for 4 weeks.The thickness of root-end cavity (3 or 5 mm) had no influence in the bacterial leakage of the root end filled with MTA. Removing the smear layer may not be necessary in root-end cavities filled with MTA.