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OBJECTIVES: This study is aimed to evaluate the compatibility of single-cone filling technique in reciprocal and rotationally formed canals in using Micro-CT (Micro-computed tomography). MATERIALS AND METHODS: The mesiolingual and mesiobuccal canals of the mesial roots of 30 mandibular molars were used for this study, concluding 60 root canals. The samples were split into two groups, 30 of which were shaped with the HyFlex EDM system and 30 with the WaveOne Gold system. In both groups, one of the canals of the shaped roots was filled with the lateral compaction and the other with a matched single-cone technique with a bioceramic-based root canal sealer, BioRoot RCS. The percentage of voids in the canal were evaluated by micro-CT radiograph before and after obturation. RESULTS: Regardless of the kinematics used, the single-cone technique left significantly fewer voids than the lateral compaction. In the regional analysis, the groups filled with the single-cone technique had significantly better results than the lateral compaction group in the middle and coronal thirds. In the kinematics comparison, the group shaped with the reciprocal WaveOne Gold system and filled with the single-cone system had the best results. CONCLUSIONS: The reciprocal nickel-titanium (NiTi) system is more effective shaping method than the rotational NiTi system. The matching single-cone technique had significantly better results than the lateral compaction technique. CLINICAL RELEVANCE: According to results of this study, matching single-cone technique has more successful results than the lateral compaction.