Marginal adaptation and internal porosity characteristics of root-end filling materials are important factors determining their clinical performance. The aim of this study was to quantitatively evaluate the marginal adaptation to radicular dentin (interfacial void volume) and internal porosity volume of a novel mineral trioxide aggregate brand using micro-CT analysis. Ten extracted upper central incisors were selected, instrumented, and obturated. Roots were resected at the apical 3 mm, and root-end cavities were prepared ultrasonically and filled with Harvard MTA. SkyScan 1272 micro-CT equipment was used to scan the specimens at a resolution of 6 μm, and three-dimensional images were reconstructed. All volumetric porosity parameters of the tested material were calculated in absolute (mm3) and relative values (%), as follows: open porosity volume (OPV), closed porosity volume (CPV), and total porosity volume (TPV). The mean OPV and OPV% found for Harvard MTA were 0.0268 mm3 and 0.91%, respectively. The mean CPV and CPV% were 0.0283 mm3 and 0.94%, respectively. The TPV and TPV% were 0.0569 mm3 and 1.85%. There was no significant difference between the OPV% and CPV% (p < 0.05). In conclusion, when applied as a retrofilling material, Harvard MTA exhibited excellent marginal adaptation to the dentin with minimal interfacial voids and internal microporosity. Therefore, this new calcium silicate brand may be considered an efficient alternative to conventional products.