Aim: This study aimed to use the micro-computed tomography to evaluate the interfacial adaptation and the presence of gaps of NeoMTA Plus, BioRoot RCS, and MTA in the root-end cavities. Methodology: Thirty standardized bovine roots measuring 15 mm in length were selected. Chemical-mechanical preparation was performed up to instrument #80 and obturation with the cold lateral compaction technique with cement based on zinc oxide and eugenol. The roots were kept at 37º C for seven days. Afterward, apicectomy of the apical 3mm and a root-end filling cavity was performed at 3mm depth. Micro-computed tomography (micro-CT) was performed to measure the volume of the retroactivity. The roots were divided by stratified randomization into three groups according to the retro-end filling material: NeoMTA Plus, BioRoot RCS, and MTA. A new micro-CT was performed to assess the presence of voids in the root-end filling material and between it and the canal wall. One-way ANOVA and Tukey tests were performed using the BioEstat 4.0 program. Results: There was no difference in the initial volume values of the root-end cavities (P > 0.05). After the insertion of root-end filling materials, the most significant volumes of voids were observed in the NeoMTA Plus group (P < 0.05), with no difference for the BioRoot RCS and MTA Angelus groups (P > 0.05). Conclusion: Micro-computed tomography showed that MTA and BioRoot RCS have better interfacial adaptation and presented fewer number of gaps than NeoMTA Plus when used as root-end filling materials.