This study aimed at evaluating the volume of gaps and voids, and the total porosity percentage of three calcium‐silicate‐based materials in mandibular molars apicoectomy by Micro‐CT analysis. Thirty‐three mesial roots of extracted human mandibular molars were instrumented and obturated. The apical 3mm of each root was resected and prepared. Root‐end cavities were filled with EndoSequence BC Putty (BC); ProRoot MTA (MTA) and Biodentine (BIO). Samples were scanned using a Micro‐CT scanner and the tridimensional images reconstructed. Percentage of gaps (VG%) and of voids (VV%) were obtained. Porosity percentage (Po%) was also assessed. Data were analysed using Student’s t‐test (P < 0.05). All materials presented gaps and voids. VG% was 2.006 (BC), 1.882 (MTA) and 1.450 (BIO), and VV% was 0.039 (BC), 0.021 (MTA) and 0.024 (BIO) with no statistical difference. Po% were 56.73 (BC), 51.94 (MTA) and 50.45 (BIO), with BC being statistically (P > 0.05) more porous.