We compared the apical seals of two new calcium silicate-based sealers (iRoot SP and MTA Fillapex) in the presence and absence of a smear layer. Eighty-two human premolars were prepared and randomly divided into four groups. In groups 1 and 3, the smear layer was retained. In groups 2 and 4, the root canals were irrigated with EDTA to remove the smear layer. Canals were filled using gutta-percha/iRoot SP (in groups 1 and 2) or obturated with gutta-percha/MTA Fillapex (in groups 3 and 4). Fluid filtration was used to evaluate apical microleakage. The presence of the smear layer had no significant effect on the sealing properties of the filling materials, except for iRoot SP at 2 weeks (P = 0.007). There was significantly less microleakage with iRoot SP than with MTA Fillapex (P = 0.025 at 2 weeks; P < 0.001 at 3 months). Leakage decreased significantly over time in all specimens, except in group 2 (P = 0.473). In conclusion, removal of the smear layer had no adverse effect on the sealing properties of calcium silicate-based sealers. In addition, the sealing ability of iRoot SP was superior to that of MTA Fillapex. (J Oral Sci 56, 215-219, 2014)